Semi-rational engineering of an amino acid racemase that is stabilized in aqueous/organic solvent mixtures

Enzymes are industrially applied under increasingly diverse environmental conditions that are dictated by the efforts to optimize overall process efficiency. Engineering the operational stability of biocatalysts to enhance their half-lives under the desired process conditions is a widely applied strategy to reduce costs. Here, we present a simple method to enhance enzyme stability in the presence of monophasic aqueous/organic solvent mixtures based on the concept of strengthening the enzyme's surface hydrogen-bond network by exchanging surface-located amino acid residues for arginine. Suitable residues are identified from sequence comparisons with homologous enzymes from thermophilic organisms and combined using a shuffling approach to obtain an enzyme variant with increased stability in monophasic aqueous/organic solvent mixtures. With this approach, we increase the stability of the broad-spectrum amino acid racemase of Pseudomonas putida DSM 3263 eightfold in mixtures with 40% methanol and sixfold in mixtures with 30% acetonitrile.     

Kinetic resolution of chiral amines with omega-transaminase using an enzyme-membrane reactor

A kinetic resolution process for the production of chiral amines was developed using an enzyme-membrane reactor (EMR) and a hollow-fiber membrane contactor with (S)-specific omega-transaminases (omega-TA) from Vibrio fluvialis JS17 and Bacillus thuringiensis JS64. The substrate solution containing racemic amine and pyruvate was recirculated through the EMR and inhibitory ketone product was selectively extracted by the membrane contactor until enantiomeric excess of (R)-amine exceeded 95%. Using the reactor set-up with flat membrane reactor (10-mL working volume), kinetic resolutions of alpha-methylbenzylamine (alpha-MBA) and 1-aminotetralin (200 mM, 50 mL) were carried out. During the operation, concentration of ketone product, i.e., acetophenone or alpha-tetralone, in a substrate reservoir was maintained below 0.1 mM, suggesting efficient removal of the inhibitory ketone by the membrane contactor. After 47 and 32.5 h of operation using 5 U/mL of enzyme, 98.0 and 95.5% ee of (R)-alpha-MBA and (R)-1-aminotetralin were obtained at 49.5 and 48.8% of conversion, respectively. A hollow-fiber membrane reactor (39-mL working volume) was used for a preparative-scale kinetic resolution of 1-aminotetralin (200 mM, 1 L). After 133 h of operation, enantiomeric excess reached 95.6% and 14.3 g of (R)-1-aminotetralin was recovered (97.4% of yield). Mathematical modeling of the EMR process including the membrane contactor was performed to evaluate the effect of residence time. The simulation results suggest that residence time should be short to maintain the concentration of the ketone product in EMR sufficiently low so as to decrease conversion per cycle and, in turn, reduce the inhibition of the omega-TA activity.     

Organic solvent tolerance and thermostability of a β-glucosidase co-engineered by random mutagenesis

Random mutagenesis was applied for development of organic solvent tolerant β-glucosidase I (BGLI) of Pichia etchellsii to extend its use for glyco-conjugate synthesis in non-aqueous medium. Previously cloned BGL1 encoding β-glucosidase I (BGLI) was subjected to error prone PCR and the mutant library was cloned in pPIC9 followed by transformation into Pichia pastoris. Transformants were first selected for functional β-glucosidase phenotype followed by screening for organic solvent tolerance in acetonitrile, dimethylformamide, dimethyl sulfoxide, methanol, 2-propanol. One of the enzyme variants, named, OT-BGLI exhibited 1.7- to 10-fold higher stability in 20–30% (v/v) methanol, 2-propanol, dimethylformamide compared to the wild type enzyme. This property was also accompanied by higher thermostability of the enzyme in aqueous buffer solution. Three of the six mutations (other 3 being silent) were mapped in the non-conserved regions of the gene. Modeled structure of the enzyme pin pointed increased hydrogen bonds, intra-ionic interactions (contributed by G414D and N789D replacements), facilitated proton exchange in organic solvents (contributed by Y722H) to be the causative agents for enhanced organic solvent stability and thermostability. Secondary structure of the mutant enzyme was similar to the wild type enzyme. Simultaneous enhanced organic solvent and thermal stability makes this enzyme an ideal candidate for glycoconjugate synthesis in aqueous-organic solvent systems.     

Synthesis of the kyotorphin precursor benzoyl‐L‐tyrosine‐L‐argininamide with immobilized α‐chymotrypsin in sequential batch with enzyme reactivation

α‐Chymotrypsin was immobilized in activated agarose support and the stability of the biocatalyst was assessed in three polar organic solvents, namely, ethanol, diglyme, and acetonitrile. Ethanol was the solvent in which the stability of the enzyme was higher and was then selected to perform the synthesis of the kyotorphin derivative benzoyl‐tyrosine argininamide, evaluating enzyme reactivation after synthesis. Substrates for reaction were benzoyl tyrosine ethyl ester and argininamide, the reaction being performed under kinetic control. High conversion yield (85%) was obtained and the immobilized enzyme was successfully used in sequential batch reactor operation with enzyme reactivation after three batches. © 2015 American Institute of Chemical Engineers Biotechnol. Prog., 32:54–59, 2016     

Fluorescence and circular dichroism spectroscopy of cytochrome c in alkylammonium formate ionic liquids

The structural stability of cytochrome c has been studied in alkylammonium formate (AAF) ionic liquids such as methylammonium formate (MAF) and ethylammonium formate (EAF) by fluorescence and circular dichroism (CD) spectroscopy. At room temperature, the native structure of cytochrome c is maintained in relatively high ionic liquid concentrations (50-70% AAF/water or AAF/phosphate buffer pH 7.0) in contrast with denaturation of cytochrome c in similar solutions of methanol or acetonitrile with water or buffer cosolvents. Fluorescence and CD spectra indicate that the conformation of cytochrome c is maintained in 20% AAF-80% water from 30 to 50 °C. No such temperature stability is found in 80% AAF-20% water. About one-third of the enzyme activity of cytochrome c in 80% AAF-20% water can be maintained as compared with phosphate buffer, and this is greater than the activities measured in corresponding methanol and acetonitrile aqueous solutions. This biophysical study shows that AAFs have potential application as organic solvent replacements at moderate temperature in the mobile phase for the separation of proteins in their native form by reversed phase liquid chromatography.     

Structure and activity of alpha-chymotrypsin and trypsin in aqueous organic media

The effects of different concentrations (20-95%) of organic solvents (ethanol, 1,4-dioxane and acetonitrile) were studied on alpha-chymotrypsin and trypsin from bovine pancreas. The changes in secondary structure were followed by CD measurements, and the apparent Michaelis constants (KMapp) and the stabilities of the enzymes were determined. Significant alterations in the CD spectra were found for both enzymes at the different organic solvent concentrations. The apparent KM values of trypsin and alpha-chymotrypsin decreased as the low solvent concentrations were elevated, but then increased in the presence of higher organic solvent concentrations. The stabilities of the enzymes changed on increase of the organic solvent concentration; trypsin exhibited a higher stability than that of alpha-chymotrypsin in all organic solvents. These results show that at an organic solvent content of 95% the manifestation of an enzyme activity similar to that measured in water can be attributed to the similar compositions of the secondary structural elements.     

Effects of water miscible organic solvents on the activity and conformation of the Baeyer-Villiger monooxygenases from Thermobifida fusca and Acinetobacter calcoaceticus: a comparative study

A broader exploitation of enzymes in organic synthesis can be achieved by increasing their tolerance toward organic solvents. In this study, the stability and activity of Baeyer–Villiger monooxygenases from Thermobifida fusca (PAMO) and Acinetobacter sp. (CHMO) in the presence of water miscible organic solvents were compared. PAMO was more stable than CHMO. The concentration of solvent (v/v) at which it halved its activity (C₅₀) was 4‐ to 16‐fold higher than that observed for CHMO. For PAMO, the C₅₀ varied from 16% to 55% of solvent and followed the destabilizing order methanol < ethanol < 1,4‐dioxane < acetonitrile < trifluoroethanol. In the case of CHMO, the maximal C₅₀ was 7% with methanol and even lower with the other solvents. Therefore, methanol was the most tolerated solvent. In the case of PAMO, methanol induced a significant increase of enzyme activity (up to fivefold), which was optimal at 20% (v/v) solvent. Only minor spectral variations were observed with PAMO in 20% methanol, suggesting that the increase of activity observed in this condition is not due to marked conformational changes. Fluorescence and circular dichroism analyses showed that the lower stability of CHMO toward organic solvent correlates with a more pronounced destructive effect on its secondary and tertiary structure. A possible rationale for the higher stability of PAMO could be inferred from inspection of the PAMO and CHMO (two enzymes of similar size) structure, which revealed a higher (up to twofold) number of ionic bridges in PAMO with respect to CHMO. Biotechnol. Bioeng. 2011; 108:491–499. © 2010 Wiley Periodicals, Inc.     

Continuous production of kyotorphin

The continuous alpha-chymotrypsin-catalyzed peptide synthesis of kyotorphin, tyrosyl-arginine, via the N(alpha) formyltyrosyl-arginine propyl ester is described. For continuous process development, two reaction systems were studied: immobilized alpha-chymotrypsin covalently bound to Eupergit C packed in a column, and soluble alpha-chymotrypsin utilizing an enzyme membrane reactor. Selectivities and kinetic parameters are discussed. The use of soluble enzyme in an enzyme membrane reactor proved superior to the covalently immobilized enzyme. A significant loss of enzyme activity and a certain decrease of selectivity was observed during immobilization. It was shown that the addition of organic solvent, in this case n-propanol, causes a severe diminuation of the enzyme activity.     

Effects of water content on the tetrahedral intermediate of chymotrypsin - trifluoromethylketone in polar and non-polar media: observations from molecular dynamics simulation

The work uses MD simulation to study effects of five water contents (3 %, 10 %, 20 %, 50 %, 100 %?v/v) on the tetrahedral intermediate of chymotrypsin - trifluoromethyl ketone in polar acetonitrile and non-polar hexane media. The water content induced changes in the structure of the intermediate, solvent distribution and H-bonding are analyzed in the two organic media. Our results show that the changes in overall structure of the protein almost display a clear correlation with the water content in hexane media while to some extent U-shaped/bell-shaped dependence on the water content is observed in acetonitrile media with a minimum/maximum at 10–20 % water content. In contrast, the water content change in the two organic solvents does not play an observable role in the stability of catalytic hydrogen-bond network, which still exhibits high stability in all hydration levels, different from observations on the free enzyme system [Zhu L, Yang W, Meng YY, Xiao X, Guo Y, Pu X, Li M (2012) J Phys Chem B 116(10):3292–3304]. In low hydration levels, most water molecules mainly distribute near the protein surface and an increase in the water content could not fully exclude the organic solvent from the protein surface. However, the acetonitrile solvent displays a stronger ability to strip off water molecules from the protein than the hexane. In a summary, the difference in the calculated properties between the two organic solvents is almost significant in low water content (<10 %) and become to be small with increasing water content. In addition, some structural properties at 10?~?20 %?v/v hydration zone, to large extent, approach to those in aqueous solution.

Racemization of undesired enantiomers: Immobilization of mandelate racemase and application in a fixed bed reactor

Production of optically pure products can be based on simple unselective synthesis of racemic mixtures combined with a subsequent separation of the enantiomers; however, this approach suffers from a 50% yield limitation which can be overcome by racemization of the undesired enantiomer and recycling. Application of biocatalyst for the racemization steps offers an attractive option for high‐yield manufacturing of commercially valuable compounds. Our work focuses on exploiting the potential of racemization with immobilized mandelate racemase. Immobilization of crude mandelate racemase via covalent attachment was optimized for two supports: Eupergit^® CM and CNBr‐activated Sepharose 4 Fast Flow. To allow coupling of enzymatic reaction with enantioselective chromatography, a mobile phase composition compatible with both processes was used in enzymatic reactor. Kinetic parameters obtained analyzing experiments carried out in a batch reactor could be successfully used to predict fixed‐bed reactor performance. The applicability of the immobilized enzyme and the determined kinetic parameters were validated in transient experiments recording responses to pulse injections of R‐mandelic acid. The approach investigated can be used for futher design and optimization of high yield combined resolution processes. The characterized fixed‐bed enzymatic reactor can be integrated e.g. with chromatographic single‐ or multicolumn steps in various configurations.     

Expression, purification, refolding and characterization of a putative lysophospholipase from Pyrococcus furiosus: retention of structure and lipase/esterase activity in the presence of water-miscible organic solvents at high temperatures

A putative lysophospholipase (PF0480) encoded by the Pyrococcus furiosus genome has previously been cloned and expressed in Escherichia coli. Studies involving crude extracts established the enzyme to be an esterase; however, owing presumably to its tendency to precipitate into inclusion bodies, purification and characterization have thus far not been reported. Here, we report the overexpression and successful recovery and refolding of the enzyme from inclusion bodies. Dynamic light scattering suggests that the enzyme is a dimer, or trimer, in aqueous solution. Circular dichroism and fluorescence spectroscopy show, respectively, that it has mixed beta/alpha structure and well-buried tryptophan residues. Conformational changes are negligible over the temperature range of 30–80 °C, and over the concentration range of 0–50% (v/v) of water mixtures with organic solvents such as methanol, ethanol and acetonitrile. The enzyme is confirmed to be an esterase (hydrolyzing p-NP-acetate and p-NP-butyrate) and also shown to be a lipase (hydrolyzing p-NP-palmitate), with lipolytic activity being overall about 18- to 20-fold lower than esterase activity. Against p-NP-palmitate the enzyme displays optimally activity at pH 7.0 and 70 °C. Remarkably, over 50% activity is retained at 70 °C in the presence of 25% acetonitrile. The high organic solvent stability and thermal stability suggest that this enzyme may have useful biodiesel-related applications, or applications in the pharmaceutical industry, once yields are optimized.     

An integrated process: ester synthesis in an enzymatic membrane reactor and water sorption

In the case of such reactions as ester synthesis, water is produced during the reaction. Because these reactions are carried out in hydrophobic solvents an additional (water) phase in the system must not be allowed, i.e. the concentration of water saturation in the organic solvent should not be exceeded. In such a case, the reaction kinetics and product equilibrium concentration undergo undesirable changes because of the partition coefficient of the components and hampered process of product separation. Hence, removal of the water produced in the reaction determines whether the process is successful or not. For this purpose, the integrated process with water sorption in the column with molecular sieves was applied. Integration of the process of synthesis and dehydration of a reaction phase, in which a biocatalyst is suspended and not dissolved as in water solutions, requires holding up of the catalyst in the reactor before directing the stream of reaction mixture to dehydration process. This hold-up and a possibility of multiple use of the catalyst may be accomplished by using a separating barrier, e.g. an ultrafiltration membrane or by permanent fixing of the catalyst to the matrix, e.g. a polymeric membrane. The efficiency and activity of a biocatalyst (lipase CAL-B) immobilized on a polymer membrane by sorption and chemical binding, were determined. A subject of study was the synthesis of geranyl acetate, one of the most known aromatic compound. A hydrophobic (polypropylene) matrix was shown to be a much better carrier in the reactions performed in an organic solvent than a hydrophilic (polyamide) membrane being tested. The reaction kinetics of geranyl acetate synthesis with the use of geraniol and acetic acid as substrates, was described by the equation defining the "Ping-Pong Bi Bi" mechanism that was related additionally to the inhibition of a substrate (acetic acid). The following constants of kinetic equation were obtained k(3)(')=0.344 mol g(-1)h(-1), K(mA)=0.257 mol l(-1), K(mG)=1.629 and K(iA)=0.288 for the native enzyme and v(max,Gel)=111.579 mol l(-1)h(-1), K(mA)=0.255 mol l(-1), K(mG)=1.91 mol l(-1), K(iA)=0.238 mol l(-1) for the one immobilized by sorption on a polypropylene membrane. Half-life time of the native enzyme activity was 204 h and stability of the immobilized preparation was 70 h. With respect to the reaction kinetics and stability of the native enzyme and immobilized preparation, from both types of membrane bioreactor more attractive appears to be the one in which the membrane is used not as a catalyst layer but only as a barrier that immobilizes the native enzyme within the bioreactor volume. When an integrated process proceeds, the method to collect water in the sorption column during the process, appeared to work very well. The reaction proceeded with a very high efficiency (after 120 h alpha=98.2% for native enzyme and 83.2% for immobilized enzyme) and due to low water concentration in the system ( approximately 0.000% v/v) the second phase was not created.     

Catalysis of protease/cyclodextrin complexes in organic solvents: Effects of reaction conditions and cyclodextrin structure on catalytic activity of proteases

α-Chymotrypsin (CT) was lyophilized from an aqueous solution in the presence of hydroxypropyl-β-cyclodextrin (HP-β-CyD). The enzyme preparation was used as a catalyst for transesterification between N-acetyl-l-tyrosine ethyl ester and methanol in a mixed solvent of acetonitrile/water (97/3 (v/v)). The enzyme preparation had much higher catalytic activity than free CT. The activity increased with an increase of HP-β-CyD/CT ratio and reached a maximum activity at the weight ratio of 4. Also, the activity of HP-β-CyD/CT increased with an increase in water content in the reaction media, and the maximum activity was obtained at 5–10% water. The fluorescence spectroscopic analysis suggested that the co-lyophilization with HP-β-CyD increased the structural stability of CT in acetonitrile/water. Upon co-lyophilization with HP-β-CyD, the activity of CT increased in any of the solvents used, but the activity depended strongly on the nature of the organic solvents. The catalytic activity of subtilisin Carlsberg (STC) also increased by co-lyophilization with α-, β-, γ-CyD or tri-O-methyl-β-CyD. α-CyD gave the best result, while HP-β-CyD diminished the activity of STC.     

Influence of Water Miscible Organic Solvents on α-chymotrypsin in Solution and Immobilized on Eupergit CM

The effects of the water-miscible organic solvents (methanol, ethanol, 1-propanol, 2-propanol, acetonitrile, N,N′-dimethylformamide and tetrahydrofuran) on the stability and catalytic activity of α-chymotrypsin (CT) immobilized on Eupergit CM were studied. Enhanced stabilities and activities were observed both as a consequence of immobilization and the presence of organic solvent, which in combination provide long term (at least 24 h) retention of activity, and up to 50-fold increase in 50% (v/v) methanol in buffer. Low quantities (20%, v/v) of acetonitrile not only prevented CT inactivation by autolysis at 20°C but also induced a significant increase in the activity of both free (six-fold) and immobilized (two-fold) CT.Linus Olofsson and Pernilla Söderberg authors have contributed equally to the work.     

Ionic liquids as alternative co-solvents for laccase: study of enzyme activity and stability

The activity and stability of commercial laccase (DeniLite base) in three different water soluble ionic liquids (ILs) (1-ethyl-3-methylimidazolium 2-(2-methoxyethoxy) ethylsulfate, [emim][[MDEGSO4], 1-ethyl-3-methylimidazolium ethylsulfate, [emim][EtSO4], and 1-ethyl-3-methylimidazolium methanesulfonate, [emim][MeSO3]) have been studied and compared to that in two organic solvents (acetonitrile and dimethyl sulfoxide). Initial enzyme activities were similar among the ILs if the same conditions were used. A high reduction on initial enzyme activity was found with acidic pH (5.0). The effect of pH and solvent concentration on enzyme stability were investigated in more detail for 1 week. The enzyme maintained a high stability at pH 9.0 for all ILs tested. [emim][MDEGSO4] was the most promising IL for laccase with an activity loss of about 10% after 7 days of incubation. The kinetic studies in the presence of ABTS as substrate allowed to calculate the Michaelis- Menten parameters. Good agreement was found between experimental data and calculated values using the Michaelis-Menten mechanism, with a total average relative deviation of 2.1%.     

A caveat for the use of log P values for the assessment of the biocompatibility of organic solvents

The degree of enzyme deactivation for lipases from Candida rugosa and Pseudomonas sp., hydroxynitrile lyase and mandelate racemase upon exposure to organic solvents can be correlated to their respective partition coefficients (log P values). However, three unexpected results were obtained: (1) the deactivation exerted by protic solvents, e.g., methanol, is severely underestimated; (2) little deactivation by an organic solvent cannot neccessarily be correlated to catalytic activity in this medium, and (3) in contrast to other enzymes, hydroxynitrile lyase is exceptionally stable towards deactivation by DMF.     

Stability of free and immobilised peroxidase in aqueous–organic solvents mixtures

The activity and stability of horseradish (Amoracia rusticana) peroxidase (HRP) free in solution and immobilised onto silica microparticles was studied in the presence of organic co-solvents.

The effect of several hydrophilic organic solvents, namely dimethyl sulfoxide, dimethylformamide, dioxan, acetonitrile and tetrahydrofuran, in the activity and stability of free HRP was studied. From the solvents tested, DMSO led to the highest activities and stabilities. After 2 h of incubation at 35°C, the remaining activity of the enzyme in the presence of 30% of each solvent was less than 30%, with exception of DMSO for which the enzyme remained fully active.

In order to increase stability, HRP was covalently immobilised onto silica microparticles. The half-life of the enzyme in buffer at 50°C increased from 2 to 52 h when the enzyme was immobilised. The stability of both free and immobilised HRP was also studied at 50°C in aqueous mixtures of 3.5, 20, 35 and 50% (v/v) DMSO. Free HRP stability was not affected by the presence of 3.5 and 20% DMSO, but higher contents lead to a more pronounced deactivation. Immobilised HRP stability increased with DMSO content up to 20%, decreasing for higher contents. The enzyme half-life increased more than 300% when changing from buffer to 20% DMSO.

The deactivation of free HRP was modelled using the simple exponential decay, and the deactivation of immobilised HRP was described by a two-step inactivation model.     

Effect of organic solvents on the activity and stability of halophilic alcohol dehydrogenase (ADH2) from Haloferax volcanii

The effect of various organic solvents on the catalytic activity, stability and substrate specificity of alchohol dehydrogenase from Haloferax volcanii (HvADH2) was evaluated. The HvADH2 showed remarkable stability and catalysed the reaction in aqueous?Corganic medium containing dimethyl sulfoxide (DMSO) and methanol (MeOH). Tetrahydrofuran and acetonitrile were also investigated and adversely affected the stability of the enzyme. High concentration of salt, essential to maintain the enzymatic activity and structural integrity of the halophilic enzyme under standard conditions may be partially replaced by DMSO and MeOH. The presence of organic solvents did not induce gross changes in substrate specificity. DMSO offered a protective effect for the stability of the enzyme at nonoptimal pHs such as 6 and 10. Salt and solvent effects on the HvADH2 conformation and folding were examined through fluorescence spectroscopy. The fluorescence findings were consistent with the activity and stability results and corroborated the denaturing properties of some solvents. The intrinsic tolerance of this enzyme to organic solvent makes it highly attractive to industry.     

Papain in organic solvents: determination of conditions suitable for biocatalysis and the effect on substrate specificity and inhibition

Synthesis of N-CBZ-(N-Carbobenzoxy)-1-amino-acid methyl esters from N-CBZ-amino acids and methanol has been used as an assay to examine the properties of papain in organic solvents containing small amounts of water. Papain is active in solvents ranging in polarity from acetonitrile to tetrachloromethane. The optimal activity in each solvent varied only about three to four fold, but the amount of added water required to achieve it varied from 4% (v/v) in acetonitrile to 0.05% (v/v) in tetrachloromethane. The enzyme was generally more stable in hydrophobic solvents and at lower water contents. The apparent K(m) value of CBZ-glycine was 26 times higher in acetonitrile than in toluene due to differential partitioning of the substrate between aqueous and organic phases. The substrate specificity of the enzyme was qualitatively little different from that in aqueous solution, with amino acid derivatives still the best substrates. Nitrile analogs of substrates inhibited the enzyme, as they do in aqueous solution, and inhibition by a variety of substituted aromatic hydrocarbons showed that the main specificity of papain for hydrophobic side chains at its S(2) subsite, was little affected. The results show that papain can catalyze reactions under a variety of conditions in organic solvents but its substrate specificity is little changed from that in aqueous media.