No description available.

Engineering artificial cells is currently an emerging area of research that involves constructing mimics of biological cells. These biomimetic cellular systems hold tremendous promise for the different biomedical applications (diagnostics, therapy, tissue engineering, gene transfection, bioactive coatings) as well as aspects of synthetic biology. A key architectural principle of the cell is a multicompartmentalized assembly, which is one of the features of biological cells that enable the performance of multiple complex biochemical reactions within confined environments. For this purpose, this study demonstrates novel artificial cells, not only presenting organelle mimics but also incorporating various stimuli for regulating enzymatic cascade reactions within the artificial cell and for controlled simultaneous and/or subsequent release of the encapsulated (therapeutic) molecules. To successfully fabricate the multifunctional polymeric multicompartmentalized systems as artificial cells aimed for, in the first step a hollow capsule as biomimetic cellular membrane was developed to simulate a key characteristic of functional artificial cells for the selective uptake and release of (bio)molecules and particles for intra- and intercellular signaling processes. Herein using LbL technique which involved alternate deposition of oppositely charged polyelectrolytes on silica template via electrostatic interaction, the pH and temperature dual-responsive and photo-crosslinked hollow capsule was fabricated and they can be used for the subsequent post-encapsulation process of protein-like macromolecules (≤ 11 nm) and their controllable release triggered by external stimuli for mimicking the controllable bio-inspired functions of cell membranes. The reversible temperature and pH dual-response ability of the hollow capsules has been analyzed. The uptake and release properties of the resulting hollow capsules with different degree of photo-crosslinking for cargos have been further investigated at various temperatures (25, 37 or 45°C) and pH (5.5 or 7.4) of the solution. Next, the design of the polymersomal subcompartmens as organelle mimics, which divide the interior of the multicompartmentalized systems into subcompartments and can stably encapsulate fragile hydrophobic and hydrophilic cargo, e.g., enzymes in order to conduct encapsulated catalysis-resembling cell organelles, was also an important subject. The fabrication of these subcompartments was starting with the synthesis of suitably end-group block copolymers to realize the enzyme-loaded, multifunctional, pH-responsive, photo-crosslinked and post-labelled polymersomes decorated with adamantane groups. The pH sensitivity and various enzymatic reactions of the established multifunctional Ada-polymersomes have been investigated. Based on the above concepts, a bottom-up approach was developed to assemble a structural and functional eukaryotic cell mimics, including “membrane-associated” multicompartmentalized system (MS1) and “free-floating” multicompartmentalized system (MS2), by loading pH-sensitive Ada-polymersomes inside the multifunctional cell membrane. The creation of these multicompartmentalized systems was based on the assembly of enzyme-loaded Ada-polymersomes as organelle mimics onto sacrificial particle templates by host-guest interaction, followed by the LbL deposition of temperature-responsive and photo-crosslinkable PMA(β-CD)/[PAH/PNMD]3 multilayers and outer protective capping PAH/PMA(PEG) bilayer as biomimetic cellular membrane. Upon photo-crosslinking the polymer biomimetic membrane and dissolution of the particle templates, multicompartmentalized systems were obtained. Spatial position of the subcompartments can be controlled using non-covalent host-guest concept, which yielded multicompartmentalized systems containing “membrane-associated” and “free-floating” subunits. Moreover, the metabolism mimicry of multicompartmentalized systems by performing multiple successive two-enzyme cascade reactions in the cells and the multiple parallel reactions by using a third enzyme for deactivating the reaction product and interfering the cascade reaction have been investigated. In conclusion, these multicompartmentalized systems, combining the advantages of both pH-responsive Ada-polymersomes as organelle mimics and multifunctional hollow capsule as biomimetic cellular membrane, present new opportunities for the development of functional cell mimics. The presented studies highlight crucial aspects for the successful applications of such cell mimics for diagnostics, tissue engineering, as nanoreactors, as carriers for multiple drug delivery with controlled release profiles, or as therapeutic artificial cells.

Multifunctional enzymes have alternative functions or activities, known as “moonlighting” or “promiscuous”, which are often hidden behind a native enzyme activity and therefore only visible under special environmental conditions. In this thesis, the active-site of Pseudozyma (formerly Candida) antarctica lipase B was explored for a promiscuous conjugate addition activity. Pseudozyma antarctica lipase B is a lipase industrially used for hydrolysis or transacylation reactions. This enzyme contains a catalytic triad, Ser105-His224-Asp187, where a nucleophilic attack from Ser105 on carboxylic acid/ester substrates cause the formation of an acyl enzyme. For conjugate addition activity in Pseudozyma antarctica lipase B, replacement of Ser105 was assumed necessary to prevent competing hemiacetal formation. However, experiments revealed conjugate addition activity in both wild-type enzyme and the Ser105Ala variant. Enzyme-catalyzed conjugate additions were performed by adding sec-amine, thiols or 1,3-dicarbonyl compounds to various α,β-unsaturated carbonyl compounds in both water or organic solvent. The reactions followed Michaelis-Menten kinetics and the native ping pong bi bi reaction mechanism of Pseudozyma antarctica lipase B for hydrolysis/transacylation was rerouted to a novel ordered bi uni reaction mechanism for conjugate addition (Paper I, II, III). The lipase hydrolysis activity was suppressed more than 1000 times by the replacement of the nucleophilic Ser105 to Ala (Paper III).

No description available.

No description available.

Ground state destabilization is a hypothesis to explain enzyme catalysis. The most popular interpretation of it is the entropic effect, which states that enzymes accelerate biochemical reactions by bringing the reactants to a favorable position and orientation and the entropy cost of this is compensated by enthalpy of binding. Once the enzyme-substrate complex is formed, the reaction could proceed with negligible entropy cost. Deamination of cytidine catalyzed by E.coli cytidine deaminase appears to agree with this hypothesis. In this reaction, the chemical transformation occurs with a negligible entropy cost and the initial binding occurs with a large entropy penalty that is comparable to the entropic cost of the uncatalyzed reaction. Our calculations revealed that this reaction occurs with different mechanisms in the cytidine deaminase and water. The uncatalyzed reaction involves a concerted mechanism and the entropy cost of this reaction appears to be dominated by the reacting fragments and first solvation shell. The catalyzed reaction occurs via a stepwise mechanism in which a hydroxide ion acts as the nucleophile. In the active site, the entropy cost of hydroxide ion formation is eliminated due to pre-organization of the active site. Hence, the entropic effect in this reaction is due to a pre-organized active site rather than ground state destabilization. In the second part of this thesis, we investigated peptide bond formation and peptidyl-tRNA hydrolysis at the peptidyl transferase center of the ribosome. Peptidyl-tRNA hydrolysis occurs by nucleophilic attack of a water molecule on the ester carbon of peptidyl-tRNA. Our calculations showed that this reaction proceeds via a base catalyzed mechanism where the A76 O2’ is the general base and activates the nucleophilic water. Peptide bond formation occurs by nucleophilic attack of the α-amino group of aminoacyl-tRNA on the ester carbon of peptidyl-tRNA. For this reaction we investigated two mechanisms: i) the previously proposed proton shuttle mechanism which involves a zwitterionic tetrahedral intermediate, and ii) a general base mechanism that proceeds via a negatively charged tetrahedral intermediate. Although both mechanisms resulted in reasonable activation energies, only the proton shuttle mechanism found to be consistent with the pH dependence of peptide bond formation.

A busca por materiais derivados de fontes renováveis e com características como biocompatibilidade e biodegradabilidade tem crescido significativamente nos últimos anos. A utilização de enzimas na polimerização representa um grande passo para a obtenção destes, visto que possibilitam a produção de polímeros evitando a utilização de catalisadores tóxicos e, assim, melhorando sua biocompatibilidade. O presente trabalho descreve a utilização de monômeros funcionais derivados de fontes renováveis na produção de poliésteres hidrolisáveis via catálise enzimática. As sínteses de polímeros produzidos a partir de isosorbídeo e ácidos dicarboxílicos ou derivados - como seus ésteres alquílicos e vinílicos - foram feitas utilizando a lipase de Candida antarctica Fração B como catalisador. As polimerizações foram realizadas por policondensações em massa e em solução, utilizando-se diferentes solventes e diferentes técnicas para remoção de subprodutos de reação. A principal abordagem foi o estudo das diferentes condições reacionais realizadas, variando-se o tempo de reação, tipo do monômero, solvente utilizado (se for o caso) e tipo de técnica para remoção de subprodutos visando o aumento da massa molar dos polímeros. A condição que forneceu os materiais com maiores massas molares foi a policondensação em solução, utilizando a mistura cicloexano:benzeno como solvente. Tendo por objetivo investigar profundamente a condição ótima obtida, e estabelecer padrões de comparação com outros sistemas, foram estudados, nessa condição, parâmetros como tempo de reação, efeito do tamanho da cadeia carbônica do monômero, grupo de saída, solubilidade dos polímeros e diluição do sistema. Os materiais obtidos foram caracterizados por cromatografia por exclusão de tamanho (SEC), termogravimetria (TG), calorimetria exploratória diferencial (DSC), espectroscopia no infravermelho, difração de raios-X, e Ressonância Magnética Nuclear (RMN) de 1H e 13C. Através deste trabalho foi provado que, embora apresente uma cinética de reação lenta, a polimerização enzimática deste diol secundário estericamente impedido é possível, fornecendo poliésteres com massas molares similares às obtidas via catálise química. Todos os resultados obtidos neste trabalho são inéditos no que diz respeito à polimerização enzimática de dióis secundários impedidos, mais especificamente de isosorbídeo. / The search for materials derived from renewable sources, with characteristics such as biocompatibility and biodegradability has grown significantly in recent years. The use of enzymes in the polymerization is a major step for the attainment of these materials, since it allows the production of polymers while avoiding the use of toxic catalysts and thus improving its biocompatibility. This paper describes the use of functional monomers derived from renewable sources in the production of hydrolysable polyesters by enzyme catalysis The synthesis and characterization of polymers derived from isosorbide and dicarboxilic acids or derivatives - such as alkyl and vinyl esters - were carried out using the lipase from Candida antarctica - Fraction B as catalyst. The polymerizations were accomplished by polycondensations in bulk and in solution, using different solvents and different techniques for removal of reaction byproducts. The main approach was to study the different reaction conditions, by varying the reaction time, monomer type, solvent used (if applicable) and the type of technique for removal of byproducts, aiming at maximizing polymer molar mass. The condition that provided the material with higher molecular weight was the solution step-growth polymerization, using a mixture cyclohexane:benzene as solvents. Aiming to thoroughly investigate the optimum condition obtained, and to establish standards for comparison with other systems, it was studied, in this condition, parameters such as reaction time, effect of monomer carbon chain length , leaving group, polymers solubility of and dilution of the reaction system. The materials were characterized by gel permeation chromatography (SEC), thermogravimetry (TG), differential scanning calorimetry (DSC), infrared spectroscopy, X-ray diffraction and 1H and 13C Nuclear Magnetic Resonance (NMR). Through this work it was proved that, in spite of a slow reaction kinetics, the enzymatic polymerization of this hindered secondary diol is possible, providing polyester with molecular weight similar to those obtained by chemical catalysis. All results obtained in this work are unprecedented with respect to the enzymatic polymerization of hindered secondary diols, more specifically of Isosorbide.

<p>Hybrid density functional theory (DFT) B3LYP method is applied to study the four diverse enzyme systems: <i>zinc-containing peptidases</i> (thermolysin and stromelysin),<i> methyl-coenzyme M reductase</i>, <i>ribonucleotide reductases</i> (classes I and III), and <i>superoxide dismutases</i> (Cu,Zn- and Ni-dependent enzymes). Powerfull tools of modern quantum chemistry are used to address the questions of biological pathways at their molecular level, proposing a novel mechanism for methane production by methyl-coenzyme M reductase and providing additional insights into hydrolysis by zinc peptidases, substrate conversion by ribonucleotide reductases, and biological superoxide dismutation. Catalysis by these enzymes, with the exception of zinc peptidases, involves radical chemistry.</p>

<p>In the present thesis the density functional B3LYP has been used to study reactions of NO and O₂ in redox active enzymes.</p><p>Reduction of nitric oxide (NO) to nitrous oxide (N₂O) is an important part in the bacterial energy conservation (denitrification). The reduction of NO in three different bimetallic active sites leads to the formation of hyponitrous acid anhydride (N₂O₂^2-). The stability of this intermediate is crucial for the reaction rate. In the two diiron systems, respiratory and scavenging types of NOR, it is possible to cleave the N-O bond, forming N₂O, without any extra protons or electrons. In a heme-copper oxidase, on the other hand, both a proton and an electron are needed to form N₂O.</p><p>In addition to being an intermediate in the denitrification, NO is a toxic agent. Myoglobin in the oxy-form reacts with NO forming nitrate (NO₃ ^-) at a high rate, which should make this enzyme an efficient NO scavenger. Peroxynitrite (ONOO^-) is formed as a short-lived intermediate and isomerizes to nitrate through a radical reaction.</p><p>In the mechanism for pumping protons in cytochrome oxidase, thermodynamics, rather than structural changes, might guide protons to the heme propionate for further translocation.</p><p>The dioxygenation of arachidonic acid in prostaglandin endoperoxide H synthase forms the bicyclic prostaglandin G₂, through a cascade of radical reactions. The mechanism proposed by Hamberg and Samuelsson is energetically feasible.</p>

Hybrid density functional theory (DFT) B3LYP method is applied to study the four diverse enzyme systems: zinc-containing peptidases (thermolysin and stromelysin), methyl-coenzyme M reductase, ribonucleotide reductases (classes I and III), and superoxide dismutases (Cu,Zn- and Ni-dependent enzymes). Powerfull tools of modern quantum chemistry are used to address the questions of biological pathways at their molecular level, proposing a novel mechanism for methane production by methyl-coenzyme M reductase and providing additional insights into hydrolysis by zinc peptidases, substrate conversion by ribonucleotide reductases, and biological superoxide dismutation. Catalysis by these enzymes, with the exception of zinc peptidases, involves radical chemistry.