Enzymatic enantioselective C-C-bond formation in microreactors

We have demonstrated that multiple crude enzyme lysates containing a hydroxynitrile lyase can be used for the enantioselective synthesis of cyanohydrins from aldehydes in microchannels. Using a microreactor setup, two important parameters were efficiently screened consuming only minute amounts of reagents. More importantly, results from the continuous flow reaction were fully consistent with results obtained from larger batchwise processes in which a stable emulsion was formed.     

Transient kinetic studies support refinements to the chemical and kinetic mechanisms of aminolevulinate synthase

5-Aminolevulinate synthase catalyzes the pyridoxal 5'-phosphate-dependent condensation of glycine and succinyl-CoA to produce carbon dioxide, CoA, and 5-aminolevulinate, in a reaction cycle involving the mechanistically unusual successive cleavage of two amino acid substrate alpha-carbon bonds. Single and multiple turnover rapid scanning stopped-flow experiments have been conducted from pH 6.8-9.2 and 5-35 degrees C, and the results, interpreted within the framework of the recently solved crystal structures, allow refined characterization of the central kinetic and chemical steps of the reaction cycle. Quinonoid intermediate formation occurs with an apparent pK(a) of 7.7 +/- 0.1, which is assigned to His-207 acid-catalyzed decarboxylation of the alpha-amino-beta-ketoadipate intermediate to form an enol that is in rapid equilibrium with the 5-aminolevulinate-bound quinonoid species. Quinonoid intermediate decay occurs in two kinetic steps, the first of which is acid-catalyzed with a pK(a) of 8.1 +/- 0.1, and is assigned to protonation of the enol by Lys-313 to generate the product-bound external aldimine. The second step of quinonoid decay defines k(cat) and is relatively pH-independent and is assigned to opening of the active site loop to allow ALA dissociation. The data support important refinements to both the chemical and kinetic mechanisms and indicate that 5-aminolevulinate synthase operates under the stereoelectronic control predicted by Dunathan's hypothesis.     

Enzymatic synthesis of n-butyl palmitate in a solvent-free system: RSM optimization and kinetic studies

The present paper demonstrates application of biocatalysis to the synthesis of n-butyl palmitate, a cosmetic emollient ester in a solvent-free system (SFS). Fermase CALB?10000, a commercial Candida antarctica lipase B was used to accomplish the synthesis. In order to evaluate the effect of various process parameters on the synthesis, one factor at a time methodology (OFAT) and response surface methodology (RSM) complimented with central composite design (CCD) were employed. On the basis of the results obtained in one factor at one time studies, temperature, enzyme dose, and molar ratio were chosen as significant parameters and their range was selected for RSM study. The optimized factors suggested by RSM model were, temperature –60.12?°C, enzyme dose –5% w/w, and alcohol: acid ratio –2.25:1. Under these optimized factors, the experimental conversion observed was 91.25% which was in close agreement to the model predicted conversion of 92% and the enzymes were reusable up to four cycles. A separate study was carried out in order to study the effect of palmitic acid on n-butyl palmitate synthesis and to understand the kinetic profile of n-butyl palmitate synthesis reaction. Ordered bi-bi model showed a good experimental fit to the kinetic data.     

Enzymatic grafting of chitosan onto Bombyx mori silk fibroin: kinetic and IR vibrational studies

The potential for using tyrosinase to graft the polysaccharide chitosan (Ch) onto Bombyx mori silk fibroin (SF) was examined. FT-IR spectroscopy coupled to HPLC amino acid analysis showed that mushroom tyrosinase (MT) catalyses the oxidation of tyrosine (Tyr) of SF to electrophilic o-quinones. Kinetic studies showed that only a fraction of the Tyr residues available on the SF chain were oxidized. This result was interpreted in the light of the structure assumed by SF in aqueous solution: Tyr aromatic side chain groups buried into the folded hydrophobic portions of the chain were probably less accessible to MT for steric reasons. Using slightly acidic conditions (pH 6), it was possible to modify SF under homogeneous conditions. FT-IR spectroscopy provided evidence that Ch was grafted onto MT-oxidized SF: the o-quinones were found to undergo a subsequent non-enzymatic reaction with nucleophilic amino groups of Ch via Schiff-base and Michael addition mechanisms. Various factors, i.e. reaction time, pH, MT/SF ratio, were found to influence the grafting yield. The highest grafting yield was achieved at pH 7, i.e. more favorable to MT activity rather than to Ch solubility, suggesting that the determining step of the grafting reaction is the formation of o-quinones. The FT-IR spectroscopy revealed that grafting induced a beta-sheet --> random coil conformational transition.     

Linear regression analysis for enzyme kinetic studies in toxicant interactions

A new method based on linear regression of per cent modulation in enzyme activity over substrate concentration is proposed to give an interpretative base to the influence of more than one modulator/inhibitor/toxicant, a situation commonly met with in toxicological studies-toxicant interactions. Advantages of this method over the classical kinetic methods are discussed in detail using brain Mg2+ ATPase activity of the fish Tilapia mossambica under in vitro regimes of hexachlorocyclohexane and malathion.     

Metabolic pathway analysis and kinetic studies for production of nattokinase in Bacillus subtilis

We have constructed a reaction network model of Bacillus subtilis. The model was analyzed using a pathway analysis tool called elementary mode analysis (EMA). The analysis tool was used to study the network capabilities and the possible effects of altered culturing conditions on the production of a fibrinolytic enzyme, nattokinase (NK) by B. subtilis. Based on all existing metabolic pathways, the maximum theoretical yield for NK synthesis in B. subtilis under different substrates and oxygen availability was predicted and the optimal culturing condition for NK production was identified. To confirm model predictions, experiments were conducted by testing these culture conditions for their influence on NK activity. The optimal culturing conditions were then applied to batch fermentation, resulting in high NK activity. The EMA approach was also applied for engineering B. subtilis metabolism towards the most efficient pathway for NK synthesis by identifying target genes for deletion and overexpression that enable the cell to produce NK at the maximum theoretical yield. The consistency between experiments and model predictions proves the feasibility of EMA being used to rationally design culture conditions and genetic manipulations for the efficient production of desired products.     

Multidigestion in continuous flow tandem protease-immobilized microreactors for proteomic analysis

Proteolysis by sequence-specific proteases is the key step for positive sequencing in proteomic studies integrated with mass spectrometry (MS). The conventional method of in-solution digestion of protein is a time-consuming procedure and has limited sensitivity. In this study, we report a simple and rapid system for the analysis of protein sequence and protein posttranslational modification by multienzymatic reaction in a continuous flow using the enzyme (trypsin, chymotrypsin, or alkaline phosphatase)-immobilized microreactor. The feasibility and performance of the single microreactor and tandem microreactors that were connected by the different microreactors were determined by the digestion of nonphosphoprotein (cytochrome c) and phosphoproteins (β-casein and pepsin A). The single microreactor showed rapid digestion compared with that of in-solution digestions. Multiple digestion by the tandem microreactors showed higher sequence coverage compared with that by in-solution or the single microreactor. Moreover, the tandem microreactor that was made by using the combination of protease-immobilized microreactor and phosphatase-immobilized microreactor showed the capability for phosphorylation site analysis in phosphoproteins without the use of any enrichment strategies or radioisotope labeling techniques. This approach provides a strategy that can be applied to various types of linking microreactor-based multienzymatic reaction systems for proteomic analysis.     

Proteolysis approach without chemical modification for a simple and rapid analysis of disulfide bonds using thermostable protease‐immobilized microreactors

Disulfide bonds in proteins are important not only for the conformational stability of the protein but also for the regulation of oxidation–reduction in signal transduction. The conventional method for the assignment of disulfide bond by chemical cleavage and/or proteolysis is a time‐consuming multi‐step procedure. In this study, we report a simple and rapid analysis of disulfide bond from protein digests that were prepared by the thermostable protease‐immobilized microreactors. The feasibility and performance of this approach were evaluated by digesting lysozyme and BSA at several temperatures. The proteins which stabilize their conformations by disulfide bonds were thermally denatured during proteolysis and were efficiently digested by the immobilized protease but not by free protease. The digests were directly analyzed by ESI‐TOF MS without any purification or concentration step. All four disulfide bonds on lysozyme and 10 of 17 on BSA were assigned from the digests by the trypsin‐immobilized microreactor at 50°C. The procedure for proteolysis and the assignment were achieved within 2 h without any reduction and alkylation procedure. From the present results, the proteolysis approach by the thermostable protease‐immobilized microreactor provides a strategy for the high‐throughput analysis of disulfide bond in proteomics.     

Adaptive stochastic-deterministic chemical kinetic simulations

MOTIVATION: Biochemical signaling pathways and genetic circuits often involve very small numbers of key signaling molecules. Computationally expensive stochastic methods are necessary to simulate such chemical situations. Single-molecule chemical events often co-exist with much larger numbers of signaling molecules where mass-action kinetics is a reasonable approximation. Here, we describe an adaptive stochastic method that dynamically chooses between deterministic and stochastic calculations depending on molecular count and propensity of forward reactions. The method is fixed timestep and has first order accuracy. We compare the efficiency of this method with exact stochastic methods. RESULTS: We have implemented an adaptive stochastic-deterministic approximate simulation method for chemical kinetics. With an error margin of 5%, the method solves typical biologically constrained reaction schemes more rapidly than exact stochastic methods for reaction volumes >1-10 micro m(3). We have developed a test suite of reaction cases to test the accuracy of mixed simulation methods. AVAILABILITY: Simulation software used in the paper is freely available from http://www.ncbs.res.in/kinetikit/download.html     

Enzymatic hydrolysis of cellulosic materials: A kinetic study

A kinetic study of the enzymatic hydrolysis of two celluloses with different structural features was performed at various temperatures (26-50 degrees C). The enzymatic system consisted of three types of enzymes: E(1)-beta-1,4-glucan glucanohydrolase; E(2)-beta-1,4-glucan cellobiohydrolase; and E(3)-beta-glucosidase. A mathematical model for the mechanism of the hydrolysis of cellulosic materials catalyzed by a multienzymatic system was checked and a good rationalization of the experimental results was achieved. Uncompetitive and competitive glucose inhibition on E(1) and E(2), respectively, appeared to occur for both substrates. Inhibition by cellobiose was checked at 34 degrees C on one substrate. The V(max), K(m), and glucose inhibition constants were optimized and their dependence on temperature determined.     

An HPLC system for the automatic sampling and analysis of time-series kinetic studies

Robotics were used to automate a high performance liquid chromatography (HPLC) system which was designed for the unattended sampling and analysis of time-series kinetic studies. The system allowed for the direct injection of samples containing whole cells and particulates witout plugging the analytical column. Coarse debris was removed from the injected sample by a 0.5 μm inline filter. Finer particulates were removed by a guard column that was layered with three different size packing resins. To demonstrate the system's capabilities, data are presented from an 8 day progress curve showing the anaerobic biodegradation of p-cresol by a sulfate-reducing enrichment. On fitting the data to the Michaelis-Menten equation by nonlinear regression, the apparent kinetic constants K_m and V_max were calculated to be 126 μM and 4.0 μM/h, respectively, for p-cresol metabolism by the enrichment.     

Immobilized glutamate oxaloacetate transaminase. Steady state kinetic analysis and stability studies.

1. Glutamate oxaloacetate transaminase (L-aspartate: 2-oxoglutarate aminotransferase, EC 2.6.1.1) was immobilized on amino ethyl cellulose using the bifunctional reagent diethyl adipimidate. 2. The steady state kinetic analysis was performed for the particulate and the free enzyme, and the Michaelis constants measured for the amino ethyl cellulose derivative were not greatly different from those measured for the free glutamate oxaloacetate transaminase, while the latter were in good agreement with values in the literature. 3. The amino ethyl cellulose-glutamate oxaloacetate transaminase was slightly more stable than the free enzyme at 65 degrees C, but was stabilised less by polyethylene glycol than the free enzyme.     

The catalytic activity of horse spleen apoferritin. Preliminary kinetic studies and the effect of chemical modification

1. Horse spleen apoferritin catalyses the oxidation of Fe(2+) to Fe(3+) with molecular O(2) as electron acceptor under conditions where a number of other proteins have no such effect. The product is similar to ferritin by a number of criteria. 2. The progress curve is hyperbolic and the increase in initial velocity is linear with increasing apoferritin concentration. With respect to Fe(2+) the reaction follows Michaelis-Menten kinetics. The pH-dependence of the reaction was determined between pH4.3 and 6.0. 3. Modification of both tryptophan residues/apoferritin subunit with 2-nitrophenylsulphenyl chloride does not affect either k(cat.) or K(m) for the oxidation. Neither does the guanidination of seven out of nine lysine residues/subunit, the modification of nine out of ten arginine residues/subunit with cyclohexanedione, or the nitration of one out of five tyrosine residues/subunit with tetranitromethane. 4. The carboxymethylation of two out of three cysteine residues/subunit and of one out of six histidine residues/subunit can be achieved with iodoacetic acid. This carboxymethylated apoferritin is completely inactive in Fe(2+) oxidation. 5. Apoferritin does not take up Fe(3+). It appears from these results that Fe(2+) is the form in which iron is taken up by ferritin in a reaction where the protein acts as an enzyme which traps the product in the interior of the protein shell.     

Enzymatic reaction kinetic: comparison in an organic solvent and in supercritical carbon dioxide

Myristic acid esterification has been performed by an immobilized lipase from Mucor Miehei both in n-hexane and in supercritical carbon dioxide (SCCO(2)). The enzyme is stable in SCCO(2) at 15 MPa and 323 K. The reaction rate is influenced by the concentration of water and by the reaction medium composition. A reaction mechanism is proposed, and kinetic parameters are determined at 12.5 MPa and 313 K. Maxium velocity appears 1.5-fold higher in SCCO(2) than in n-hexane; however, as solubility of myristic acid is greater in n-hexane, it is not yet definitively clear that the supercritical medium is more favorable than the classical organic solvent for this type of enzyme reaction.