Improving enzymes by using them in organic solvents

Non-aqueous green solvents improve alpha-amylase induced fiber opening in leather processing

Severe water deficit and highly polluting effluent generation from leather industries have constantly been pressurizing the tanners to adopt cleaner leather processing systems. The present study aims to minimize the use of water by substituting it with non-aqueous green solvents and also to enhance the enzyme action in alpha-amylase based fiber opening process. The activity of alpha-amylase in select non-aqueous green solvents namely, heptane, polyethylene glycol 200 and propylene glycol is considerably higher by 62, 38 and 31% than in water, respectively. Comparable results are obtained for the catalytic efficiency of alpha-amylase and hence it is further validated in collagen fiber opening trials as well. Scanning electron micrographs, histological images and proteoglycan estimation supported the above findings at 1% alpha-amylase dosage. The final quality of the experimental leathers in terms of physical and bulk properties is comparable to that of control leathers. Recycling studies indicate that it is possible to replace water with green solvents for enzymatic fiber opening with the feasibility to recover more than 85% solvent-enzyme mixture and reuse without any additional alpha-amylase usage. Reduction in pollution load coupled with the efficient catalytic action of enzyme in non-aqueous media favors the present protocol for industrial applications.

Amphiphilic mPEG-Modified Oligo-Phenylalanine Nanoparticles Chemoenzymatically Synthesized via Papain

Amphiphilic mPEG-modified peptide nanoparticles were developed from oligo-phenylalanine (OPhe) nanoparticles (NPs) synthesized via papain. Tyndall effects indicate that OPhe NPs are amphiphobic. Addition of protein perturbants, sodium dodecyl sulfate (SDS), and urea, in the dispersion solution of OPhe NPs can significantly reduce the R _h,m value of NPs, from approximately 749.2 nm to about 200 nm. Therefore, the hydrophobic interaction and hydrogen bonding play major roles in maintaining the aggregation of OPhe NPs. Using the "grafting to" method, the methoxypolyethylene-modified OPhe NPs (mPEG-g-OPhe NPs) were synthesized and characterized by Fourier transform infrared spectroscopy (FTIR), ¹H NMR, electrospray ionization mass spectrometry (ESI-MS), and dynamic light scattering (DLS). The attenuated total reflectance (ATR) spectrum of OPhe NPs and mPEG-g-OPhe NPs demonstrate that the secondary structures of these NPs are mainly β-type. mPEG-g-OPhe NPs can self-aggregate into spherical micelles both in water and cyclohexane. Increasing the chain length of the mPEG moiety, the critical micellar concentrations of mPEG-g-OPhe NPs increased in water but decreased in cyclohexane. The light stability, thermal stability, hydrolysis stability, and encapsulation stability of curcumin were significantly promoted by encapsulation in the micelles formed by mPEG-g-OPhe NPs. The protective effects regularly varied with the variations in the mPEG chain length of mPEG-g-OPhe NPs.

Nucleophilic Transformations of Lewis Acid-Activated Disubstituted Epoxides with Catalyst-Controlled Regioselectivity

Due to their inherent ring strain and electrophilicity, epoxides are highly attractive building blocks for fundamental organic reactions. However, controlling the regioselectivity of disubstituted epoxide transformations is often particularly challenging. Most Lewis acid-mediated processes take advantage of intrinsic steric or electronic substrate bias to influence the site of nucleophilic attack. Therefore, the scope of many of these systems is frequently quite limited. Recent efforts to generate catalysts that can overcome substrate bias have expanded the synthetic utility of these well-known reactions. In this Perspective, we highlight various regioselective transformations of disubstituted epoxides, emphasizing those that have inspired the production of challenging, catalyst-controlled processes.

Glycosyl hydrolase catalyzed glycosylation in unconventional media

The reversible hydrolytic property of glycosyl hydrolases (GHs) as well as their acceptance of aglycones other than water has provided the abilities of GHs in synthesizing glycosides. Together with desirable physiochemical properties of glycosides and their high commercial values, research interests have been aroused to investigate the synthetic other than the hydrolytic properties of GHs. On the other hand, just like the esterification processes catalyzed by lipases, GH synthetic effectiveness is strongly obstructed by water both thermodynamically and kinetically. Medium engineering by involving organic solvents can be a viable approach to alleviate the obstacles caused by water. However, as native hydrolyases function in water-enriched environments, most GHs display poor catalytic performance in the presence of organic solvents. Some GHs from thermophiles are more tolerant to organic solvents due to their robust folded structures with strong residue interactions. Other than native sources, immobilization, protein engineering, employment of surfactant, and lyophilization have been proved to enhance the GH stability from the native state, which opens up the possibilities for GHs to be employed in unconventional media as synthases. KEY POINTS: • Unconventional media enhance the synthetic ability but destabilize GHs. • Viable approaches are discussed to improve GH stability from the native state. • GHs robust in unconventional media can be valuable industrial synthases.

Chitosan-based CLEAs from Aspergillus niger type A feruloyl esterase: high-productivity biocatalyst for alkyl ferulate synthesis

The enzymatic synthesis of alkyl ferulates is an important reaction in cosmetic and pharmaceutical chemistries, since it may allow to expand the biorefinery concept valorizing biomass wastes enriched in ferulic acid. However, robust biocatalysts for that purpose are scarce. Herein, we have immobilized the type A feruloyl esterase from Aspergillus niger (AnFaeA) as cross-linked enzyme aggregates, employing chitosan as co-feeder (ChCLEAs). High immobilization yields and relative activity recovery were attained in all assessed conditions (> 93%). Furthermore, we enhanced the thermal stability of the soluble enzyme 32-fold. AnFaeA-ChCLEAs were capable to quantitatively perform the solvent-free direct esterification of short- to medium-chain alkyl ferulates (C4-C12) in less than 24 h. By raising the operational temperature to 50 °C, AnFaeA-ChCLEAs transformed 350 mM ferulic acid into isopentyl ferulate with a space-time yield of 46.1 g of product × L^-1 × day^-1, 73-fold higher than previously reported. The overall sustainability of this alkyl ferulate production bioprocess is supported by the high total turnover number (TTN 7 × 10⁵) and the calculated green metrics (E factor = 30). Therefore, we herein present a robust, efficient, and versatile heterogeneous biocatalyst useful for the synthesis of a wide diversity of alkyl ferulates. KEY POINTS: • CLEAs of feruloyl esterase A from A. niger using chitosan as co-feeder were obtained. • Microenvironment of the biocatalysts allowed to obtain C1 to C18 alkyl ferulates. • Biocatalyst at boundary conditions showed a high productivity of 46 g/L day. Graphical Abstract.

Enzyme dynamics: Looking beyond a single structure

Conventional understanding of how enzymes function strongly emphasizes the role of structure. However, increasing evidence clearly indicates that enzymes do not remain fixed or operate exclusively in or close to their native structure. Different parts of the enzyme (from individual residues to full domains) undergo concerted motions on a wide range of time-scales, including that of the catalyzed reaction. Information obtained on these internal motions and conformational fluctuations has so far uncovered and explained many aspects of enzyme mechanisms, which could not have been understood from a single structure alone. Although there is wide interest in understanding enzyme dynamics and its role in catalysis, several challenges remain. In addition to technical difficulties, the vast majority of investigations are performed in dilute aqueous solutions, where conditions are significantly different than the cellular milieu where a large number of enzymes operate. In this review, we discuss recent developments, several challenges as well as opportunities related to this topic. The benefits of considering dynamics as an integral part of the enzyme function can also enable new means of biocatalysis, engineering enzymes for industrial and medicinal applications.

What do we learn from enzyme behaviors in organic solvents? - Structural functionalization of ionic liquids for enzyme activation and stabilization

Enzyme activity in nonaqueous media (e.g. conventional organic solvents) is typically lower than in water by several orders of magnitude. There is a rising interest of developing new nonaqueous solvent systems that are more "water-like" and more biocompatible. Therefore, we need to learn from the current state of nonaqueous biocatalysis to overcome its bottleneck and provide guidance for new solvent design. This review firstly focuses on the discussion of how organic solvent properties (such as polarity and hydrophobicity) influence the enzyme activity and stability, and how these properties impact the enzyme's conformation and dynamics. While hydrophobic organic solvents usually lead to the maintenance of enzyme activity, solvents carrying functional groups like hydroxys and ethers (including crown ethers and cyclodextrins) can lead to enzyme activation. Ionic liquids (ILs) are designable solvents that can conveniently incorporate these functional groups. Therefore, we systematically survey these ether- and/or hydroxy-functionalized ILs, and find most of them are highly compatible with enzymes leading to high activity and stability. In particular, ILs carrying both ether and tert-alcohol groups are among the most enzyme-activating solvents. Future direction is to learn from enzyme behaviors in both water and nonaqueous media to design biocompatible "water-like" solvents.

Activity and specificity studies of the new thermostable esterase EstDZ2

In this paper, we study the activity and specificity of EstDZ2, a new thermostable carboxyl esterase of unknown function, which was isolated from a metagenome library from a Russian hot spring. The biocatalytic reaction employing EstDZ2 proved to be an efficient method for the hydrolysis of aryl p-, o- or m-substituted esters of butyric acid and esters of secondary alcohols. Docking studies revealed structural features of the enzyme that led to activity differences among the different substrates.

Synthesis of Hydrophobic Propionyl Neohesperidin Ester Using an Immobilied Enzyme and Description of Its Anti-proliferative and Pro-apoptotic Effects on MCF-7 Human Breast Cancer Cells

Neohesperidin (NH) is a natural flavonoid glycoside compound with considerable physiological and pharmacological activities. However, its bioavailability is limited due to poor solubility, and few studies have so far attempted improve the solubility and bioavailability of NH. In this study, we structurally modified NH using an immobilized lipase to improve lipophilicity and therefore expand its applicability in lipophilic media as well as enhance its bioavailability in vivo. In addition, we aimed investigated the pro-apoptoptotic activity of this new compound (propionyl neohesperidin ester, PNHE) in MCF-7 breast cancer cells using a variety of cellular assays, including the MTT (3-(4, 5-dimethyl- 2-thiazolyl)-2, 5-diphenyl-2-h-tetrazolium bromide assay, assessment of intracellular reactive oxygen species (ROS) levels, and flow cytometry. We successfully synthesized PNHE using immobilized lipases, and the esterification of NH was confirmed by Fourier transform-infrared spectroscopy (FT-IR). Compared to NH, HNPE showed higher anti-proliferative and pro-apoptotic in MCF-7 breast cancer cells, which may be explained by its increased lipophilicity compared to neohesperidin, benefiting to the action of NH on the cancer cell wall. The IC₅₀ of PNHE for inducing apoptosis of MCF-7 cells was 185.52 μg/mL. PNHE increased both the proportion of cells in Sub-G1 phase and the cellular ROS content, indicating a certain therapeutic effect of HNPE on breast cancer.

Generation of Stilbene Antimicrobials against Multiresistant Strains of Staphylococcus aureus through Biotransformation by the Enzymatic Secretome of Botrytis cinerea

The biotransformation of a mixture of resveratrol and pterostilbene was performed by the protein secretome of Botrytis cinerea. Several reaction conditions were tested to overcome solubility issues and to improve enzymatic activity. Using MeOH as cosolvent, a series of unusual methoxylated compounds was generated. The reaction was scaled-up, and the resulting mixture purified by semipreparative HPLC-PDA-ELSD-MS. Using this approach, 15 analogues were isolated in one step. Upon full characterization by NMR and HRMS analyses, eight of the compounds were new. The antibacterial activities of the isolated compounds were evaluated in vitro against the opportunistic pathogens Pseudomonas aeruginosa and Staphylococcus aureus. The selectivity index was calculated based on cytotoxic assays performed against human liver carcinoma cells (HepG2) and the human breast epithelial cell line (MCF10A). Some compounds revealed remarkable antibacterial activity against multidrug-resistant strains of S. aureus with moderate human cell line cytotoxicity.

Lyophilized Cell-Free Systems Display Tolerance to Organic Solvent Exposure

Cell-free systems offer a powerful way to deliver biochemical activity to the field without cold chain storage. These systems are capable of sensing as well as biosynthesis of useful molecules at the point of need. So far, cell-free protein synthesis (CFPS) reactions have been studied as aqueous solutions in test tubes or absorbed into paper or cloth. Embedding biological functionality into broadly used materials, such as plastic polymers, represents an attractive goal. Unfortunately, this goal has for the most part remained out of reach, presumably due to the fragility of biological systems outside of aqueous environments. Here, we describe a surprising and useful feature of lyophilized cell-free lysate systems: tolerance to a variety of organic solvents. Screens of individual CFPS reagents and different CFPS methods reveal that solvent tolerance varies by CFPS reagent composition. Tolerance to suspension in organic solvents may facilitate the use of polymers to deliver dry cell-free reactions in the form of coatings or fibers, or allow dosing of analytes or substrates dissolved in nonaqueous solvents, among other processing possibilities.

Using nature's blueprint to expand catalysis with Earth-abundant metals

Numerous redox transformations that are essential to life are catalyzed by metalloenzymes that feature Earth-abundant metals. In contrast, platinum-group metals have been the cornerstone of many industrial catalytic reactions for decades, providing high activity, thermal stability, and tolerance to chemical poisons. We assert that nature's blueprint provides the fundamental principles for vastly expanding the use of abundant metals in catalysis. We highlight the key physical properties of abundant metals that distinguish them from precious metals, and we look to nature to understand how the inherent attributes of abundant metals can be embraced to produce highly efficient catalysts for reactions crucial to the sustainable production and transformation of fuels and chemicals.

Molecular Dynamics Insights into the Nanoscale Structural Organization and Local Interaction of Aqueous Solutions of Ionic Liquid 1-Butyl-3-methylimidazolium Nitrate

Considering the growing number of applications of the aqueous ionic liquids (ILs), atomistic molecular dynamics (MD) simulations were used to probe the effect of water molar fraction, x_w, ranging from 0.00 to 0.90, on the nanoscale local structure of 1-butyl-3-methylimidazolium nitrate, [bmim][NO₃], IL. The results prove that, with water addition, the cation-anion, cation-cation, and anion-anion structural correlations are weakened, while strong anion-water and unconventional cation-water hydrogen bonds are formed in the solutions. Water molecules were detected as bridges between nitrate anions, and the water cluster size distribution at different x_w's was investigated. Simulation shows a similar pattern of probability densities for water and anion around the acidic hydrogen atoms of the reference cation ring, while both species move away from the cation butyl chain. Increasing the water concentration to x_w = 0.90 causes decreasing of the local arrangement of the nearest-neighboring cations, because of the weakening of cation-cation π-π stacking. In addition, this dilution reduces the probability of the in-plane cation-anion conformation, disrupts both the polar ionic network and nonpolar domains, and diminishes the nanoaggregation of the cation butyl chains compared to those of the neat IL. These results can rationalize the origins of the fluidity enhancements and transport property trends upon adding water to the imidazolium-based ILs. The current study proposes a deep atomistic-level insight into the complex coupling between water concentration, microscopic structure, and local interactions of aqueous imidazolium-based ILs with hydrophilic anions.

Unraveling How Ethanol-Induced Conformational Changes Affect BSA Protein Adsorption onto Silica Surfaces

Protein adsorption at solid-liquid interfaces is highly relevant to a wide range of applications such as biosensors, drug delivery, and pharmaceuticals. Understanding how protein conformation in bulk solution impacts adsorption behavior is fundamentally important and could also lead to the development of improved protein-based coatings. To date, relevant studies have been conducted in aqueous solutions, while it remains largely unknown how organic solvents and more specifically solvent-induced conformational changes might influence protein adsorption. Herein, using the quartz crystal microbalance-dissipation (QCM-D) and localized surface plasmon resonance (LSPR) techniques, we systematically investigated the real-time adsorption behavior of bovine serum albumin (BSA) protein onto silica surfaces in different water-ethanol mixtures ranging from 0 to 60% (v/v) ethanol. The results showed that there was greater protein adsorption at higher ethanol fractions in the 10-30% range, while more complex adsorption profiles were observed in the 40-60% range. The combination of QCM-D and LSPR measurements led us to further identify specific cases in water-ethanol mixtures where washing steps caused densification of the adsorbed protein layer as opposed to typical desorption of weakly adsorbed molecules in aqueous conditions. We discuss mechanistic factors that drive these overall adsorption trends by taking into account how ethanol fraction affects BSA conformation in bulk solution. Together, our findings demonstrate that BSA proteins can adsorb onto silica surfaces across a wide range of water-ethanol mixture conditions, while specific adsorption profiles depended on the ethanol fraction in a manner closely linked to solution-phase conformational properties.

Enzyme-Coated Micro-Crystals: An Almost Forgotten but Very Simple and Elegant Immobilization Strategy

The immobilization of enzymes using protein coated micro-crystals (PCMCs) was reported for the first time in 2001 by Kreiner and coworkers. The strategy is very simple. First, an enzyme solution must be prepared in a concentrated solution of one compound (salt, sugar, amino acid) very soluble in water and poorly soluble in a water-soluble solvent. Then, the enzyme solution is added dropwise to the water soluble solvent under rapid stirring. The components accompanying the enzyme are called the crystal growing agents, the solvent being the dehydrating agent. This strategy permits the rapid dehydration of the enzyme solution drops, resulting in a crystallization of the crystal formation agent, and the enzyme is deposited on this crystal surface. The reaction medium where these biocatalysts can be used is marked by the solubility of the PCMC components, and usually these biocatalysts may be employed in water soluble organic solvents with a maximum of 20% water. The evolution of these PCMC was to chemically crosslink them and further improve their stabilities. Moreover, the PCMC strategy has been used to coimmobilize enzymes or enzymes and cofactors. The immobilization may permit the use of buffers as crystal growth agents, enabling control of the reaction pH in the enzyme environments. Usually, the PCMC biocatalysts are very stable and more active than other biocatalysts of the same enzyme. However, this simple (at least at laboratory scale) immobilization strategy is underutilized even when the publications using it systematically presented a better performance of them in organic solvents than that of many other immobilized biocatalysts. In fact, many possibilities and studies using this technique are lacking. This review tried to outline the possibilities of this useful immobilization strategy.

γ-Glutamyltranspeptidase from Bacillus amyloliquefaciens: transpeptidation activity enhancement and L-theanine production

L-theanine, a unique amino acid in green tea with health benefits, can be enzymatically synthesized by γ-glutamyltranspeptidase (γ-GT; EC 2.3.2.2). Here, a salt-tolerant γ-glutamyltranspeptidase from a marine bacterium Bacillus amyloliquefaciens was expressed in Escherichia. coli BL21 (DE3) and was shown to be optimally active at 55 °C, pH 8.5 and alkali stable. A mutant, with higher transpeptidation activity, was obtained following two rounds of directed evolution using error-prone PCR and site-saturation mutagenesis. The mutation increased the ratio of transpeptidation to hydrolysis from 1.6 to 35.6. Additionally, Kinetic analysis exhibited 17.5% decrease of K_m, 13.0-fold increase of K_cat, and 16.3-fold increase of K_cat/K_m in mutant V319A/S437 G versus the wild-type. The 3-D modelling analysis revealed a tighter binding pocket in mutant V319A/S437 G. The frequency of hydrogen bond between donor substrate and two residues in the catalytic pocket (Gly437 and Thr375) was enhanced, which stabilized the ligand binding and thus improved the catalytic efficiency. The optimal conditions for the biocatalytic synthesis were determined as pH 10.0, 20 μg mL^-1BaGT, 200 mM L-glutamine, 2 M ethylamine, and a reaction time of 5 h. The V319A/S437 G mutant was shown to increase the percentage yield of L-theanine from 58% to 83%. These results indicate the great potential of V319A/S437 G in L-theanine production after further study.

Study on effects of co-solvents on the structure of DhaA by molecular dynamics simulation

With the increasing application of enzymes in various research fields, the choices of co-solvents in enzymatic preparations which directly related to the catalytic activity have been attracted attention. Thus, researching on the stabilization or destabilization behaviors of enzymes in different solvents is extremely essential. In this study, the structural changes of DhaA in two typical aprotic co-solvents (acetonitrile and tetrahydrofuran) were firstly investigated by molecular dynamics (MD) simulation. The simulation results revealed the strong van der Waals force between co-solvents and DhaA which could induce the structural change of enzyme. Interestingly, the differences of molecular size and the electrostatic force with enzyme of two co-solvents led to quite different influences on DhaA. As for acetonitrile, solvent molecules could penetrate into the catalytic site of DhaA which promoted by the electrostatic interaction. On the contrary, tetrahydrofuran molecules were mainly distributed around the catalytic site due to the relative weak electrostatic interaction and steric resistance effect. It can be concluded that different co-solvent can affect the key domains, substrate pathway and catalytic pocket of DhaA.Communicated by Ramaswamy H. Sarma.

The Use of Ion Liquids as a Trojan Horse Strategy in Enzyme-Catalyzed Biotransformation of (R,S)-Atenolol

The enzymatic method was used for the direct biotransformation of racemic atenolol. The catalytic activities of commercially available lipases from Candida rugosa were tested for the kinetic resolution of (R,S)-atenolol by enantioselective acetylation in various two-phase reaction media containing ionic liquids. The composed catalytic system gave the possibility to easy separate substrates and products of the conducted enantioselective reaction and after specific procedure to reuse utilized enzymes in another catalytic cycle.

Organic solvent stability and long-term storage of myoglobin-based carbene transfer biocatalysts

Recent years have witnessed a rapid increase in the application of enzymes for chemical synthesis and manufacturing, including the industrial-scale synthesis of pharmaceuticals using multienzyme processes. From an operational standpoint, these bioprocesses often require robust biocatalysts capable of tolerating high concentrations of organic solvents and possessing long shelflife stability. In this work, we investigated the activity and stability of myoglobin (Mb)-based carbene transfer biocatalysts in the presence of organic solvents and after lyophilization. Our studies demonstrate that Mb-based cyclopropanases possess remarkable organic solvent stability, maintaining high levels of activity and stereoselectivity in the presence of up to 30%-50% (v/v) concentrations of various organic solvents, including ethanol, methanol, N,N-dimethylformamide, acetonitrile, and dimethyl sulfoxide. Furthermore, they tolerate long-term storage in lyophilized form, both as purified protein and as whole cells, without significant loss in activity and stereoselectivity. These stability properties are shared by Mb-based carbene transferases optimized for other type of asymmetric carbene transfer reactions. Finally, we report on simple protocols for catalyst recycling as whole-cell system and for obviating the need for strictly anaerobic conditions to perform these transformations. These findings demonstrate the robustness of Mb-based carbene transferases under operationally relevant conditions and should help guide the application of these biocatalysts for synthetic applications.

Expression and characterization of a novel organic solvent tolerant protease from Bacillus sphaericus DS11

Organic solvent-tolerant proteases have many applications in the synthesis of peptides. In this study, we have developed a low-cost and convenient method to produce highly concentrated organic solvent-tolerant protease. Organic solvent tolerant protease (OSP) gene from Bacillus sphaericus DS11 was cloned and expressed in Bacillus subtilis WB800. The optimum pH of the recombinant protease was 9.0. The optimum temperature of the recombinant protease was 40 °C. The recombinant protease was purified by ethanol with the yield of (87.33%). The yield of OSP enriched by ethanol was higher than that of by Ni-chelating affinity chromatography, which indicated that precipitation of the recombinant OSP with ethanol is a relatively low-cost and fast method for organic solvent -tolerant protease preparation. These results showed that this enzyme could be very useful in different industrial applications.

Structural and biochemical characterization of a novel thermophilic Coh01147 protease

Proteases play an essential role in living organisms and represent one of the largest groups of industrial enzymes. The aim of this work was recombinant production and characterization of a newly identified thermostable protease 1147 from thermophilum indigenous Cohnella sp. A01. Phylogenetic tree analysis showed that protease 1147 is closely related to the cysteine proteases from DJ-1/ThiJ/PfpI superfamily, with the conserved catalytic tetrad. Structural prediction using MODELLER 9v7 indicated that protease 1147 has an overall α/β sandwich tertiary structure. The gene of protease 1147 was cloned and expressed in Escherichia coli (E. coli) BL21. The recombinant protease 1147 appeared as a homogenous band of 18 kDa in SDS-PAGE, which was verified by western blot and zymography. The recombinant protein was purified with a yield of approximately 88% in a single step using Ni-NTA affinity chromatography. Furthermore, a rapid one-step thermal shock procedure was successfully implemented to purify the protein with a yield of 73%. Using casein as the substrate, K_m, and k_cat, k_cat/K_m values of 13.72 mM, 3.143 × 10⁻³ (s^-1), and 0.381 (M^-1 S^-1) were obtained, respectively. The maximum protease activity was detected at pH = 7 and 60°C with the inactivation rate constant (kin) of 2.10 × 10–3 (m^-1), and half-life (t_1/2) of 330.07 min. Protease 1147 exhibited excellent stability to organic solvent, metal ions, and 1% SDS. The protease activity was significantly enhanced by Tween 20 and Tween 80 and suppressed by cysteine protease specific inhibitors. Docking results and molecular dynamics (MD) simulation revealed that Tween 20 interacted with protease 1147 via hydrogen bonds and made the structure more stable. CD and fluorescence spectra indicated structural changes taking place at 100°C, very basic and acidic pH, and in the presence of Tween 20. These properties make this newly characterized protease a potential candidate for various biotechnological applications.

Cloning, Expression, and Structural Elucidation of a Biotechnologically Potential Alkaline Serine Protease From a Newly Isolated Haloalkaliphilic Bacillus lehensis JO-26

An alkaline protease gene of Bacillus lehensis JO-26 from saline desert, Little Rann of Kutch, was cloned and expressed in Escherichia coli BL21 (DE3). A 1,014-bp ORF encoded 337 amino acids. The recombinant protease (APrBL) with Asp 97, His 127, and Ser 280 forming catalytic triad belongs to the subtilase S8 protease family. The gene was optimally expressed in soluble fraction with 0.2 mM isopropyl β-D-thiogalactopyranoside (IPTG), 2% (w/v) NaCl at 28°C. APrBL, a monomer with a molecular mass of 34.6 kDa was active over pH 8–11 and 30°C−70°C, optimally at pH 10 and 50°C. The enzyme was highly thermostable and retained 73% of the residual activity at 80°C up to 3 h. It was significantly stimulated by sodium dodecyl sulfate (SDS), Ca²⁺, chloroform, toluene, n-butanol, and benzene while completely inhibited by phenylmethylsulfonyl fluoride (PMSF) and Hg²⁺. The serine nature of the protease was confirmed by its strong inhibition by PMSF. The APrBL gene was phylogenetically close to alkaline elastase YaB (P20724) and was distinct from the well-known commercial proteases subtilisin Carlsberg (CAB56500) and subtilisin BPN′ (P00782). The structural elucidation revealed 31.75% α-helices, 22.55% β-strands, and 45.70% coils. Although high glycine and fewer proline residues are a characteristic feature of the cold-adapted enzymes, the similar observation in thermally active APrBL suggests that this feature cannot be solely responsible for thermo/cold adaptation. The APrBL protease was highly effective as a detergent additive and in whey protein hydrolysis.

A Mesohaline Thraustochytrid Produces Extremely Halophilic Alpha-Amylases

Halophilic bacteria are well known to produce highly salt-tolerant enzymes that have unusual applications in biotechnology. Production of halophilic proteins is generally not expected in mesohaline microorganisms. Ulkenia sp. AH-2, a mesohaline, marine straminipilan thraustochytrid isolated from waters of a mangrove ecosystem, produces halophilic alpha-amylases. Four enzyme fractions, viz.., A, B, C, and D, were obtained upon ammonium sulfate fractionation and gel filtration. These had a broad salinity tolerance ranging from 0 to 4 M NaCl, with an optimum at 3 M NaCl. Pools A, C, and D each resolved as a single band on PAGE and zymogram analysis, and the purified proteins were designated Amy a, Amy c, and Amy h. The major activity resided in "pool B," consisting of several amylases which could not be further resolved into pure fractions. Together, these had an optimum at 2 M NaCl. All the enzymes were stable to storage for 2 to 24 h at 4 °C in a range of salt concentrations and even showed enhanced activity following such incubations. True to halophilic enzymes, the complex of "pool B" amylases showed improved activity in the presence of a wide range of organic solvents at 20% concentration. These enzymes are of particular interest by virtue of their constitutive nature as well as production under culture conditions that do not require salinity beyond that of seawater.

Understanding thermal and organic solvent stability of thermoalkalophilic lipases: insights from computational predictions and experiments

Bacillus thermocatenulatus lipase (BTL2), a member of the isolated lipase family known as thermoalkalophilic lipases, carries potential for industrial applications owing to its ability to catalyze versatile reactions under extreme conditions. This study investigates the molecular effects of distinct solvents on the stability of BTL2 at different temperatures, aiming to contribute to lipase use in industrial applications. Initially, molecular dynamic (MD) simulations were carried out to address for the molecular impacts of distinct solvents on the structural stability of BTL2 at different temperatures. Two lipase conformations representing the active and inactive forms were simulated in 5 solvents including water, ethanol, methanol, cyclohexane, and toluene. Low temperature simulations showed that polar solvents led to enhanced lid fluctuations compared with non-polar solvents reflecting a more dynamic equilibrium between active and inactive lipase conformations in polar solvents including water, while the overall structure of the lipase in both forms became more rigid in non-polar solvents than they were in polar solvent. Notably, the native lipase fold was maintained in non-polar solvents even at high temperatures, indicating an enhancement of lipase's thermostability in non-polar organic solvents. Next, we conducted experiments for which BTL2 was expressed in a heterologous host and purified to homogeneity, and its thermostability in different solvents was assessed. Parallel to the computational findings, experimental results suggested that non-polar organic solvents contributed to BTL2's thermostability at concentrations as high as 70% (v/v). Altogether, this study provides beneficial insights to the lipase use under extreme conditions. Graphical Abstract.

Continuous Flow Bioamination of Ketones in Organic Solvents at Controlled Water Activity using Immobilized ω-Transaminases

Compared with biocatalysis in aqueous media, the use of enzymes in neat organic solvents enables increased solubility of hydrophobic substrates and can lead to more favorable thermodynamic equilibria, avoidance of possible hydrolytic side reactions and easier product recovery. ω-Transaminases from Arthrobacter sp. (AsR-ωTA) and Chromobacterium violaceum (Cv-ωTA) were immobilized on controlled porosity glass metal-ion affinity beads (EziG) and applied in neat organic solvents for the amination of 1-phenoxypropan-2-one with 2-propylamine. The reaction system was investigated in terms of type of carrier material, organic solvents and reaction temperature. Optimal conditions were found with more hydrophobic carrier materials and toluene as reaction solvent. The system's water activity (aw) was controlled via salt hydrate pairs during both the biocatalyst immobilization step and the progress of the reaction in different non-polar solvents. Notably, the two immobilized ωTAs displayed different optimal values of aw, namely 0.7 for EziG3-AsR-ωTA and 0.2 for EziG3-Cv-ωTA. In general, high catalytic activity was observed in various organic solvents even when a high substrate concentration (450-550 mM) and only one equivalent of 2-propylamine were applied. Under batch conditions, a chemical turnover (TTN) above 13000 was obtained over four subsequent reaction cycles with the same batch of EziG-immobilized ωTA. Finally, the applicability of the immobilized biocatalyst in neat organic solvents was further demonstrated in a continuous flow packed-bed reactor. The flow reactor showed excellent performance without observable loss of enzymatic catalytic activity over several days of operation. In general, ca. 70% conversion was obtained in 72 hours using a 1.82 mL flow reactor and toluene as flow solvent, thus affording a space-time yield of 1.99 g L-1 h-1. Conversion reached above 90% when the reaction was run up to 120 hours.

High-Efficient Production of (S)-1-[3,5-Bis(trifluoromethyl)phenyl]ethanol via Whole-Cell Catalyst in Deep-Eutectic Solvent-Containing Micro-Aerobic Medium System

The ratio of substrate to catalyst (S/C) is a prime target for the application of asymmetric production of enantiomerically enriched intermediates by whole-cell biocatalyst. In the present study, an attractive increase in S/C was achieved in a natural deep-eutectic solvent (NADES) containing reaction system under microaerobic condition for high production of (S)-1-[3,5-bis(trifluoromethyl)phenyl]ethanol ((S)-3,5-BTPE) with Candida tropicalis 104. In PBS buffer (0.2 M, pH 8.0) at 200 rpm and 30 °C, 79.5 g (Dry Cell Weight, DCW)/L C. tropicalis 104 maintained the same yield of 73.7% for the bioreduction of 3,5-bis(trifluoromethyl)acetophenone (BTAP) under an oxygen-deficient environment compared with oxygen-sufficient conditions, while substrate load increased 4.0-fold (from 50 mM to 200 mM). Furthermore, when choline chloride:trehalose (ChCl:T, 1:1 molar ratio) was introduced into the reaction system for its versatility of increasing cell membrane permeability and declining BTAP cytotoxicity to biocatalyst, the yields were further increased to 86.2% under 200 mM BTAP, or 72.9% at 300 mM BTAP. After the optimization of various reaction parameters involved in the bioreduction, and the amount of biocatalyst and maltose co-substrate remained 79.5 g (DCW)/L and 50 g/L, the S/C for the reduction elevated 6.3 times (3.8 mM/g versus 0.6 mM/g). By altering the respiratory pattern of the whole-cell biocatalyst and exploiting the ChCl:T-containing reaction system, the developed strategy exhibits an attractive potential for enhancing catalytic efficiency of whole-cell-mediated reduction, and provides valuable insight for the development of whole-cell catalysis.

Significantly Enhanced Synthesis of Aromatic Esters of Arbutin Catalyzed by Immobilized Lipase in Co-solvent Systems

Highly efficient and regioselective synthesis of pharmacologically interesting aromatic esters of arbutin catalyzed by immobilized lipase from Penicillium expansum in co-solvent systems was successfully carried out. As compared to tetrahydrofuran solvent, the initial rate and substrate conversion of arbutin vanilylation were markedly enhanced in tetrahydrofuran-isopropyl ether (20%, v/v). Moreover, the effects of three reaction parameters (enzyme amount, temperature and substrate molar ratio of vinyl vanillic acid to arbutin) on 6′-O-vanilloyl-arbutin synthesis were scrutinized and the key process parameters were optimized using response surface methodology (RSM). The experimental data were fitted well to a second order polynomial model by using multiple regression analysis. The best combination of variables was 50°C, 93 U/mL and 11 for the reaction temperature, the enzyme amount and mole ratio of arbutin to vinyl vanilic acid, respectively, and which the reaction rate, substrate conversion and regioselectivity were as high as 8.2 mM/h, 93 and 99%. It was worth noting that a variety of aromatic esters of arbutin were obtained with much higher conversion (93–99%) at these optimal conditions.

Length-scale dependence of protein hydration-shell density

Here we present a computational approach based on molecular dynamics (MD) simulation to study the dependence of the protein hydration-shell density on the size of the protein molecule. The hydration-shell density of eighteen different proteins, differing in size, shape and function (eight of them are antifreeze proteins), is calculated. The results obtained show that an increase in the hydration-shell density, relative to that of the bulk, is observed (in the range of 4-14%) for all studied proteins and that this increment strongly correlates with the protein size. In particular, a decrease in the density increment is observed for decreasing protein size. A simple model is proposed in which the basic idea is to approximate the protein molecule as an effective ellipsoid and to partition the relevant parameters, i.e. the solvent-accessible volume and the corresponding solvent density, into two regions: inside and outside the effective protein ellipsoid. It is found that, within the model developed here, almost all of the hydration-density increase is located inside the protein ellipsoid, basically corresponding to pockets within, or at the surface of the protein molecule. The observed decrease in the density increment is caused by the protein size only and no difference is found between antifreeze and non-antifreeze proteins.

Quantification of diacylglycerol and triacylglycerol species in human fecal samples by flow injection Fourier transform mass spectrometry

The intestinal microbiome plays an important role in human health and disease and fecal materials reflect the microbial activity. Thus, analysis of fecal metabolites provides insight in metabolic interactions between gut microbiota and host organism. In this work, we applied flow injection analysis coupled to Fourier transform mass spectrometry (FIA-FTMS) to identify and quantify lipid species in human fecal samples. Fecal homogenates were subjected to lipid extraction and analyzed by FIA-FTMS. The analysis of different subjects revealed a vast heterogeneity of lipid species abundance. The majority of samples displayed prominent signals of triacylglycerol (TG) and diacylglycerol (DG) species that could be verified by MS2 spectra. Therefore, we focused on the quantification of TG and DG. Method validation included limit of quantification, linearity, evaluation of matrix effects, recovery, and reproducibility. The validation experiments demonstrated the suitability of the method, with exception for approximately 10% of samples, where we observed coefficients of variation higher than 15%. Impaired reproducibility was related to sample inhomogeneity and could not be improved by additional sample preparation steps. Additionally, these experiments demonstrated that compared with aqueous samples, samples containing isopropanol showed higher amounts of DG, presumably due to lysis of bacteria and increased TG lipolysis. These effects were sample-specific and substantiate the high heterogeneity of fecal materials as well as the need for further evaluation of pre-analytic conditions. In summary, FIA-FTMS offers a fast and accurate tool to quantify DG and TG species and is suitable to provide insight into the fecal lipidome and its role in health and disease.

Improving the catalytic efficiency of thermostable Geobacillus stearothermophilus xylanase XT6 by single-amino acid substitution

Directed evolution using error-prone polymerase chain reaction was employed in the current study to enhance the catalytic efficiency of a thermostable Geobacillus stearothermophilus xylanase XT6 parent. High-throughput screening identified two variants with enhanced activity. Sequencing analysis revealed the presence of a single-amino acid substitution (P209L or V161L) in each variant. The maximum activity of mutant V161L and P209L was at 85°C and 70°C, respectively. Both mutants exhibited maximum activity at pH 7. The thermal and alkaline tolerance of mutant V161L only were markedly improved. The two mutants were more resistant to ethanol inhibition than the parent. Substrate specificity of the two mutants was shifted from beechwood xylan to birchwood xylan. The potential of the two mutants to hydrolyze rice straw and sugarcane bagasse increased. Both turnover number (kcat) and catalytic efficiency (kcat/kM) increased 12.2- and 5.7-folds for variant P209L and 13- and 6.5-folds for variant V161L, respectively, towards birchwood xylan. Based on the previously published crystal structure of extracellular G. stearothermophilus xylanase XT6, V161L and P209L mutation locate on βα-loops. Conformational changes of the respective loops could potentiate the loop swinging, product release and consequently result in enhancement of the catalytic performance.

Purification and characterization of thermostable α-amylase from germinating Sword bean (Canavalia gladiata (Jacq.) DC.) seeds

The thermostable α-amylase from germinating sword bean (Canavalia gladiata (Jacq.) DC.) seeds (CgAmy) was successfully purified by a combination of ammonium sulphate fractionation and Epoxy-activated Sepharose 6B affinity chromatography. The purified α-amylase showed 507.8 fold with a specific activity of 750.0 U/mg. SDS-PAGE of the purified enzyme revealed a single protein band of 50.0 kDa. Purified enzyme was confirmed as α-amylase type by LC-MS/MS analysis and activity on specific substrate of ethylidene-pNP-G7. The CgAmy revealed extreme activity at a high temperature of 50.0-70.0°C with optimum activity at 70.0°C. The optimal pH of enzyme activity was observed at 6.0. The CgAmy exhibited stability in pH range of 5.0-8.0 and highly thermostable with a temperature of 40.0-60.0°C. The kinetic parameters K _m for hydrolysis of starch were found to be 3.12 mg/ml. The α-amylase activity was enhanced in the presence of Co²⁺ and β-mercaptoethanol. While, Na²⁺, K²⁺, Ca²⁺, Mg²⁺, Zn²⁺, Ba²⁺, Fe²⁺ and Cd²⁺ slightly inhibited α-amylase activity. Interestingly, the CgAmy displayed stability towards some organic solvents and detergents. Stability at high temperature and some metal ions, organic solvents and detergents indicated that this enzyme has potential for various applications.