On the failure of de novo-designed peptides as biocatalysts.

While the elegance and efficiency of enzymatic catalysis have long tempted chemists and biochemists with reductionist leanings to try to mimic the functions of natural enzymes in much smaller peptides, such efforts have only rarely produced catalysts with biologically interesting properties. However, the advent of genetic engineering and hybridoma technology and the discovery of catalytic RNA have led to new and very promising alternative means of biocatalyst development. Synthetic chemists have also had some success in creating nonpeptide catalysts with certain enzyme-like characteristics, although their rates and specificities are generally much poorer than those exhibited by the best novel biocatalysts based on natural structures. A comparison of the various approaches from theoretical and practical viewpoints is presented. It is suggested that, given our current level of understanding, the most fruitful methods may incorporate both iterative selection strategies and rationally chosen small perturbations, superimposed on frameworks designed by nature.

Inibição de linhagens do complexo Fusarium Graminearum por compostos naturais e sintéticos

Quando produtos alimentícios e especiarias são contaminados por micotoxinas é quase impossível detoxificar utilizando processos usuais da indústria de alimentos ou durante o preparo doméstico. Por isso, controlar o crescimento do fungo e a produção de toxinas é uma demanda para garantir a segurança alimentar. Os agrotóxicos são rotineiramente utilizados como estratégia para proteger as plantas de doenças provocadas pela contaminação fúngica. No entanto, eles estão associados a efeitos adversos ao sistema nervoso central e periférico, têm ação imunodepressora e são cancerígenos. Em virtude disso, o objetivo deste trabalho foi estudar a inibição do desenvolvimento, do potencial toxigênico e da expressão gênica de linhagens do Complexo Fusarium graminearum por compostos naturais comparativamente aos fungicidas azoxistrobina e trifloxistrobina. Do farelo de arroz, foram extraídos o γ-orizanol e os ácidos fenólicos (EFF). Das sementes de nim foram extraídos os ácidos fenólicos (EFN), totalizando três extratos naturais. A capacidade antioxidante dos extratos foi verificada pelo consumo do radical livre DPPH• , capacidade de captura do radical ABTS●+, redução do ferro e inibição da oxidação enzimática. Os mecanismos de inibição de três linhagens de F. graminearum foram avaliados através da determinação de compostos estruturais (glicosamina e ergosterol) e da atividade de enzimas do metabolismo primário (α- amilase e proteases). Foram determinadas as micotoxinas de Fusarium: deoxinivalenol (DON), 15 acetildeoxinivalenol (15AcDON), 3 acetildeoxinivalenol (3AcDON), nivalenol (NIV) e zearalenona (ZEA). A expressão dos genes Tri1 e Tri5 foi determinada a fim de verificar se ocorria modificação da expressão gênica nas linhagens do Complexo F. graminearum ocasionada pela presença dos antifúngicos. O EFF apresenta atividade antioxidante destacada em relação aos demais extratos naturais para inibir a iniciação do processo, a propagação do radical livre e a catálise enzimática. A presença dos compostos naturais mostrou efeito promissor como antifúngico para as linhagens, sendo que a concentração necessária para inibir 50% do crescimento radial das colônias (MIC50) foi 0,9 g/kg para γ-orizanol; 0,032 g/kg para EFF e 0,037 g/kg para EFN, portanto, os extratos fenólicos são mais eficazes para inibição de F. graminearum do que o γ-orizanol. Os extratos naturais afetaram as atividades das enzimas α-amilase e proteases. Também ocorreu a redução da formação de componentes estruturais (glicosamina e ergosterol). Os extratos naturais se destacaram pela capacidade de inibição de micotoxinas produzidas pela biomassa fúngica, com destaque para o EFN sobre a produção de DON, 15AcDON, 3AcDON e ZEA. Sendo assim, é possível dizer que há uma relação direta entre a atividade antioxidante na inibição do fungo e na manifestação do seu potencial toxigênico. Além disso, esse estudo contribuiu com a elucidação do mecanismo de ação dos antifúngicos naturais estudados. Ocorre modificação na expressão gênica quando a linhagem é submetida ao tratamento com antifúngico, havendo uma relação direta entre a expressão do gene Tri5 e a produção de DON.

Enzymatic toxins from snake venom: structural characterization and mechanism of catalysis

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

The repertoire of nitrogen assimilation in Rhodococcus: Catalysis, pathways and relevance in biotechnology and bioremediation

The Rhodococcus genus exhibits diverse enzymatic activity that can be exploited in the conversion of natural and anthropogenic nitrogenous compounds. This catalytic response provides a selective advantage in terms of available nutrients while also serving to remove otherwise harmful xenobiotics. This review provides a critical assessment of the literature on bioconversion of organo-nitrogen compounds with a consideration of applications in bioremediation and commercial biotechnology. By examining the major nitro-organic compounds (amino acids, amines, nitriles, amides and nitroaromatics) in turn, the considerable repertoire of Rhodococcus spp. is established. The available published enzyme reaction data is coupled with genomic characterisation to provide a molecular basis for Rhodococcus enzyme activity with an assessment of the cellular properties that aid substrate accessibility and ensure stability. The metabolic gene clusters associated with the observed reaction pathways are identified and future directions in enzyme optimisation and metabolic engineering are assessed. © 2014 Society of Chemical Industry.

Role of conformational dynamics in kinetics of an enzymatic cycle in a nonequilibrium steady state

Enzyme is a dynamic entity with diverse time scales, ranging from picoseconds to seconds or even longer. Here we develop a rate theory for enzyme catalysis that includes conformational dynamics as cycling on a two-dimensional (2D) reaction free energy surface involving an intrinsic reaction coordinate (X) and an enzyme conformational coordinate (Q). The validity of Michaelis-Menten (MM) equation, i.e., substrate concentration dependence of enzymatic velocity, is examined under a nonequilibrium steady state. Under certain conditions, the classic MM equation holds but with generalized microscopic interpretations of kinetic parameters. However, under other conditions, our rate theory predicts either positive (sigmoidal-like) or negative (biphasic-like) kinetic cooperativity due to the modified effective 2D reaction pathway on X-Q surface, which can explain non-MM dependence previously observed on many monomeric enzymes that involve slow or hysteretic conformational transitions. Furthermore, we find that a slow conformational relaxation during product release could retain the enzyme in a favorable configuration, such that enzymatic turnover is dynamically accelerated at high substrate concentrations. The effect of such conformation retainment in a nonequilibrium steady state is evaluated.

Antibody-mediated catalysis: Induction and therapeutic relevance

Abzymes are immunoglobulins endowed with enzymatic activities. The catalytic activity of an abzyme resides in the variable domain of the antibody, which is constituted by the close spatial arrangement of amino acid residues involved in catalysis. The origin of abzymes is conferred by the innate diversity of the immunoglobulin gene repertoire. Under deregulated immune conditions, as in autoimmune diseases, the generation of abzymes to self-antigens could be deleterious. Technical advancement in the ability to generate monoclonal antibodies has been exploited in the generation of abzymes with defined specificities and activities. Therapeutic applications of abzymes are being investigated with the generation of monoclonal abzymes against several pathogenesis-associated antigens. Here, we review the different contexts in which abzymes are generated, and we discuss the relevance of monoclonal abzymes for the treatment of human diseases.

Kinetic Model Study on Enzymatic Hydrolysis of Cellulose Using Artificial Neural Networks

Enzymatic hydrolysis of cellulose was highly complex because of the unclear enzymatic mechanism and many factors that affect the heterogeneous system. Therefore, it is difficult to build a theoretical model to study cellulose hydrolysis by cellulase. Artificial neural network (ANN) was used to simulate and predict this enzymatic reaction and compared with the response surface model (RSM). The independent variables were cellulase amount X-1, substrate concentration X-2, and reaction time X-3, and the response variables were reducing sugar concentration Y-1 and transformation rate of the raw material Y-2. The experimental results showed that ANN was much more suitable for studying the kinetics of the enzymatic hydrolysis than RSM. During the simulation process, relative errors produced by the ANN model were apparently smaller than that by RSM except one and the central experimental points. During the prediction process, values produced by the ANN model were much closer to the experimental values than that produced by RSM. These showed that ANN is a persuasive tool that can be used for studying the kinetics of cellulose hydrolysis catalyzed by cellulase.

Enzymatic degradation of poly(L-lactide) and poly (epsilon-caprolactone) electrospun fibers

Poly(L-lactide) (PLLA) and poly(epsilon-caprolactone) (PCL) ultrafine fibers were prepared by electrospinning. The influence of cationic and anionic surfactants on their enzymatic degradation behavior was investigated by measuring weight loss, molecular weight, crystallinity, and melting temperature of the fibers as a function of degradation time. Under the catalysis of proteinase K, the PLLA fibers containing the anionic surfactant sodium docecyl sulfate (SDS) exhibited a faster degradation rate than those containing cationic surfactant triethylbenzylammonium chloride (TEBAC), indicating that surface electric charge on the fibers is a critical factor for an enzymatic degradation. Similarly, TEBAC-containing PCL fibers exhibited a 47% weight loss within 8.5 h whereas SDS-containing PCL fibers showed little degradation in the presence of lipase PS. By analyzing the charge status of proteinase K and lipase PS under the experimental conditions, the importance of the surface charges of the fibers and their interactions with the charges on the enzymes were revealed. Consequently, a "two-step" degradation mechanism was proposed: (1) the enzyme approaches the fiber surface; (2) the enzyme initiates hydrolysis of the polymer.

Design, fabrication and characterisation of components for microfluidic enzymatic biofuel cells

The concept of a biofuel cell takes inspiration from the natural capability of biological systems to catalyse the conversion of organic matter with a subsequent release of electrical energy. Enzymatic biofuel cells are intended to mimic the processes occurring in nature in a more controlled and efficient manner. Traditional fuel cells rely on the use of toxic catalysts and are often not easily miniaturizable making them unsuitable as implantable power sources. Biofuel cells however use highly selective protein catalysts and renewable fuels. As energy consumption becomes a global issue, they emerge as important tools for energy generation. The microfluidic platforms developed are intended to maximize the amount of electrical energy extracted from renewable fuels which are naturally abundant in the environment and in biological fluids. Combining microfabrication processes, chemical modification and biological surface patterning these devices are promising candidates for micro-power sources for future life science and electronic applications. This thesis considered four main aspects of a biofuel cell research. Firstly, concept of a miniature compartmentalized enzymatic biofuel cell utilizing simple fuels and operating in static conditions is verified and proves the feasibility of enzyme catalysis in energy conversion processes. Secondly, electrode and microfluidic channel study was performed through theoretical investigations of the flow and catalytic reactions which also improved understanding of the enzyme kinetics in the cell. Next, microfluidic devices were fabricated from cost-effective and disposable polymer materials, using the state-of-the-art micro-processing technologies. Integration of the individual components is difficult and multiple techniques to overcome these problems have been investigated. Electrochemical characterization of gold electrodes modified with Nanoporous Gold Structures is also performed. Finally, two strategies for enzyme patterning and encapsulation are discussed. Several protein catalysts have been effectively immobilized on the surface of commercial and microfabricated electrodes by electrochemically assisted deposition in sol-gel and poly-(o-phenylenediamine) polymer matrices and characterised with confirmed catalytic activity.

A comparative study of the synthesis of 3-substituted catechols using an enzymatic and a chemoenzymatic method

A series of cis-dihydrodiol metabolites, available from the bacterial dioxygenase-catalysed oxidation of monosubstituted benzene substrates using Pseudomonas putida UV4, have been converted to the corresponding catechols using both a heterogeneous catalyst (Pd/C) and a naphthalene cis-diol dehydrogenase enzyme present in whole cells of the recombinant strain Escherichia coli DH5 alpha(pUC129: nar B). A comparative study of the merits of both routes to 3-substituted catechols has been carried out and the two methods have been found to be complementary. A similarity in mechanism for catechol formation under both enzymatic and chemoenzymatic conditions, involving regioselective oxidation of the hydroxyl group at C-1, has been found using deuterium labelled toluene cis-dihydrodiols. The potential, of combining a biocatalytic step (dioxygenase-catalysed cis-dihydroxylation) with a chemocatalytic step (Pd/C-catalysed dehydrogenation), into a one-pot route to catechols, from the parent substituted benzene substrates, has been realised.

Enzymatic and chemoenzymatic synthesis of arene trans-dihydrodiols

Several potential approaches to the enzyme-catalysed synthesis of arene trans-diols have been examined including epoxidation/hydrolysis, bis-benzylic hydroxylation, cis-dihydroxylation/alcohol dehydrogenation/ketone reduction, cisdihydroxylation/cis-trans isomerisation. and multi-enzyme synthesis of trans-dihydrodiol secondary metabolites from primary metabolites. The lack of general applicability of these enzymatic methods has led to the development of several chemoenzymatic routes for the synthesis of a series of trans-dihydrodiols from the readily available cis-dihydrodiol precursors. Partial hydrogenation of cis-dihydrodiol metabolites to yield the corresponding cis-tetrahydrodiols followed by a regioselective Mitsunobu inversion process gave trans-tetrahydrodiols that were in turn converted to trans-dihydrodiols. The formation of anti-benzene dioxides or iron tricarbonyl complexes from the corresponding cis-dihydrodiol precursors provided shorter and more convenient chemoenzymatic routes to trans-dihydrodiols. The application of cis-dihydrodiol metabolites of polycyclic azaarenes in the synthesis of the corresponding arene oxides followed by chemical hydrolysis provides a convenient route to trans-dihydrodiols. (C) 2002 Elsevier Science B.V. All rights reserved.

Enantioselective transesterification catalysis by Candida antarctica lipase immobilized on superparamagnetic nanoparticles

Lipase B from Candida antarctica can be directly immobilized onto functionalized superparamagnetic nanoparticles, preserving its enzymatic activity in the enantioselective transesterification of secondary alcohols, with excellent results in terms of enantiomeric discrimination. The immobilized enzyme can be easily recovered with a magnet, allowing its reuse with negligible loss of activity. (C) 2009 Elsevier Ltd. All rights reserved

Enzymatic kinetic resolution of organochalcogenides in supercritical CO(2)

1-(Phenylthio)-, 1-(phenylseleno)- and 1-(phenyltelluro)-propan-2-ol were efficiently resolved by CAL-B in sc-CO(2). (C) 2011 Elsevier Ltd. All rights reserved.

Characterization of glycerol kinase from baker's yeast: Response surface modeling of the enzymatic reaction

The present study describes a methodology of dosage of glycerol kinase (GK) from baker's yeast. The standardization of the activity of the glycerol kinase from baker's yeast was accomplished using the diluted enzymatic preparation containing glycerol phosphate oxidase (GPO) and glycerol kinase. The mixture was incubated at 60 degrees C by 15 min and the reaction was stopped by the SDS solution addition. A first set of experiments was carried out in order to investigate the individual effect of temperature (7), pH and substrate concentration (S), on GK activity and stability. The pH and temperature stability tests showed that the enzyme presented a high stability to pH 6.0-8.0 and the thermal stability were completely maintained up to 50 degrees C during 1 h. The K(m) of the enzyme for glycerol was calculated to be 2 mM and V(max) to be 1.15 U/mL. In addition, modeling and optimization of reaction conditions was attempted by response surface methodology (RSM). Higher activity values will be attained at temperatures between 52 and 56 degrees C, pH around 10.2-10.5 and substrate concentrations from 150 to 170 mM.This low cost method for glycerol kinase dosage in a sequence of reactions is of great importance for many industries, like food, sugar and alcohol. RSM showed to be an adequate approach for modeling the reaction and optimization of reaction conditions to maximize glycerol kinase activity. (C) 2007 Elsevier B.V. All rights reserved.

Microcystis aeruginosa lipids as feedstock for biodiesel synthesis by enzymatic route

The cyanobacterium Microcystis aeruginosa strain NPCD-1, isolated from sewage treatment plant and characterized as a non-microcystin producer by mass spectrometry and molecular analysis, was found to be a source of lipid when cultivated in ASM-1 medium at 25 degrees C under constant white fluorescent illumination (109 mu mol photon m(-2) s(-1)). In these conditions, biomass productivity of 46.92 +/- 3.84 mg L-1 day(-1) and lipid content of 28.10 +/- 1.47% were obtained. Quantitative analysis of fatty acid methyl esters demonstrated high concentration of saturated fatty acids (50%), palmitic (24.34%) and lauric (13.21%) acids being the major components. The remaining 50% constituting unsaturated fatty acids showed higher concentrations of oleic (26.88%) and linoleic (12.53%) acids. The feasibility to produce biodiesel from this cyanobacterial lipid was demonstrated by running enzymatic transesterification reactions catalyzed by Novozym (R) 435 and using palm oil as feedstock control. Batch experiments were carried out using tert-butanol and iso-octane as solvent. Results showed similarity on the main ethyl esters formed for both feedstocks. The highest ethyl ester concentration was related to palmitate and oleate esters followed by laurate and linoleate esters. However, both reaction rates and ester yields were dependent on the solvent tested. Total ethyl ester concentrations varied in the range of 44.24-67.84 wt%, corresponding to ester yields from 80 to 100%. Iso-octane provided better solubility and miscibility, with ester yield of 98.10% obtained at 48 h for reaction using the cyanobacterium lipid, while full conversion was achieved in 12 h for reaction carried out with palm oil. These results demonstrated that cyanobacterial lipids from M. aeruginosa NPCD-1 have interesting properties for biofuel production. (c) 2012 Elsevier B.V. All rights reserved.