SilE-R and SilE-S - DABB Proteins Catalyzing Enantiospecific Hydrolysis of Organosilyl Ethers.

Silyl ethers fulfil a fundamental role in synthetic organic chemistry as protecting groups and their selective cleavage is an important factor in their application. We present here for the first time two enzymes, SilE-R and SilE-S, which are able to hydrolyze silyl ethers. They belong to the stress-response A/B barrel domain (DABB) family and are able to cleave the Si-O bond with opposite enantiopreference. Silyl ethers containing aromatic, cyclic or aliphatic alcohols and, depending on the alcohol moiety, silyl functions as large as TBDMS are accepted. The X-ray crystal structure of SilE-R, determined to a resolution of 1.98 Ȧ, in combination with mutational studies, revealed an active site featuring two histidine residues, H8 and H79, which likely act synergistically as nucleophile and Brønsted base in the hydrolytic mechanism, which has not previously been described for enzymes. Although the natural function of SilE-R and SilE-S is unknown, we propose that these 'silyl etherases' may have significant potential for synthetic applications.

Foam fractionation Tags (F-Tags) enabling surfactant-free, activity-preserving recovery of enzymes.

Enzymes have become important tools in many industries. However, the full exploitation of their potential is currently limited by a lack of efficient and cost-effective methods for enzyme purification from microbial production. One technology that could solve this problem is foam fractionation. In this study, we show that diverse natural foam-stabilizing proteins fused as F-Tags to ß-lactamase, penicillin G acylase, and formate dehydrogenase, respectively, are able to mediate foaming and recovery of the enzymes by foam fractionation. The catalytic activity of all three candidates is largely preserved. Under appropriate fractionation conditions, especially when a wash buffer is used, some F-Tags also allow nearly complete separation of the target enzyme from a contaminating protein. We found that a larger distance between the F-Tag and the target enzyme has a positive effect on the maintenance of catalytic activity. However, we did not identify any particular sequence motifs or physical parameters that influenced performance as an F-tag. The best results were obtained with a short helical F-Tag, which was originally intended to serve only as a linker sequence. The findings of the study suggest that the development of molecular tags that enable the establishment of surfactant-free foam fractionation for enzyme workup is a promising method. KEY POINTS: • Foam-stabilizing proteins mediate activity-preserving foam fractionation of enzymes • Performance as an F-Tag is not restricted to particular structural motifs • Separation from untagged protein benefits from low foam stability and foam washings.

Extended Scope and Understanding of Zinc-Dependent Alcohol Dehydrogenases for Reduction of Cyclic α-Diketones.

Alcohol dehydrogenases (ADH) are important tools for generating chiral α-hydroxyketones. Previously, only the ADH of Thauera aromatica was known to convert cyclic α-diketones with appropriate preference. Here, we extend the spectrum of suitable enzymes by three alcohol dehydrogenases from Citrifermentans bemidjiense (CibADH), Deferrisoma camini (DecADH), and Thauera phenylacetica (ThpADH). Of these, DecADH is characterized by very high thermostability; CibADH and ThpADH convert α-halogenated cyclohexanones with increased activity. Otherwise, however, the substrate spectrum of all four ADHs is highly conserved. Structural considerations led to the conclusion that conversion of diketones requires not only the expansion of the active site into a large binding pocket, but also the circumferential modification of almost all amino acid residues that form the first shell of the binding pocket. The constellation appears to be overall highly specific for the relative positioning of the carbonyl functions and the size of the C-ring.

Lipase-Mediated Conversion of Protecting Group Silyl Ethers: An Unspecific Side Reaction.

Silyl ether protecting groups are important tools in organic synthesis, ensuring selective reactions of hydroxyl functional groups. Enantiospecific formation or cleavage could simultaneously enable the resolution of racemic mixtures and thus significantly increase the efficiency of complex synthetic pathways. Based on reports that lipases, which today are already particularly important tools in chemical synthesis, can catalyze the enantiospecific turnover of trimethylsilanol (TMS)-protected alcohols, the goal of this study was to determine the conditions under which such a catalysis occurs. Through detailed experimental and mechanistic investigation, we demonstrated that although lipases mediate the turnover of TMS-protected alcohols, this occurs independently of the known catalytic triad, as this is unable to stabilize a tetrahedral intermediate. The reaction is essentially non-specific and therefore most likely completely independent of the active site. This rules out lipases as catalysts for the resolution of racemic mixtures of alcohols through protection or deprotection with silyl groups.

Rsn-2-mediated directed foam enrichment of ß-lactamase.

Today, the availability of methods for the activity-preserving and cost-efficient downstream processing of enzymes forms a major bottleneck to the use of these valuable tools in technical processes. A promising technology appears to be foam fractionation, which utilizes the adsorption of proteins at a gas-liquid interface. However, the employment of surfactants and the dependency of the applicability on individual properties of the target molecules are considerable drawbacks. Here, we demonstrate that a reversible fusion of the large, surface-active protein Ranaspumin-2 (Rsn-2) to a ß-lactamase (Bla) enabled both surfactant-free formation of a stable foam and directed enrichment of the enzyme by the foaming. At the same time, Bla maintained 70% of its catalytic activity, which was in stark contrast to the enzyme without fusion to Rsn-2. Rsn-2 predominantly mediated adsorption. Comparable results were obtained after fusion to the structurally more complex penicillin G acylase (PGA) as the target enzyme. The results indicate that using a surface-active protein as a fusion tag might be the clue to the establishment of foam fractionation as a general method for enzyme downstream processing.

Advanced Insights into Catalytic and Structural Features of the Zinc-Dependent Alcohol Dehydrogenase from Thauera aromatica.

The asymmetric reduction of ketones to chiral hydroxyl compounds by alcohol dehydrogenases (ADHs) is an established strategy for the provision of valuable precursors for fine chemicals and pharmaceutics. However, most ADHs favor linear aliphatic and aromatic carbonyl compounds, and suitable biocatalysts with preference for cyclic ketones and diketones are still scarce. Among the few candidates, the alcohol dehydrogenase from Thauera aromatica (ThaADH) stands out with a high activity for the reduction of the cyclic α-diketone 1,2-cyclohexanedione to the corresponding α-hydroxy ketone. This study elucidates catalytic and structural features of the enzyme. ThaADH showed a remarkable thermal and pH stability as well as stability in the presence of polar solvents. A thorough description of the substrate scope combined with the resolution and description of the crystal structure, demonstrated a strong preference of ThaADH for cyclic α-substituted cyclohexanones, and indicated structural determinants responsible for the unique substrate acceptance.

Characterization and Modeling of Thermostable GH50 Agarases from Microbulbifer elongatus PORT2.

Viewing the considerable potential of marine agar as a source for the sustainable production of energy as well as nature-derived pharmaceutics, this work investigated the catalytic activity of three novel GH50 agarases from the mesophilic marine bacterium Microbulbifer elongatus PORT2 isolated from Indonesian coastal seawaters. The GH50 agarases AgaA50, AgaB50, and AgaC50 were identified through genome analysis; the corresponding genes were cloned and expressed in Escherichia coli BL21 (DE3). All recombinant agarases hydrolyzed ß-p-nitrophenyl galactopyranoside, indicating ß-glycosidase characteristics. AgaA50 and AgaB50 were able to cleave diverse natural agar species derived from Indonesian agarophytes, indicating a promising tolerance of these enzymes for substrate modifications. All three GH50 agarases degraded agarose, albeit with remarkable diversity in their catalytic activity and mode of action. AgaA50 and AgaC50 exerted exolytic activity releasing differently sized neoagarobioses, while AgaB50 showed additional endolytic activity in dependence on the substrate size. Surprisingly, AgaA50 and AgaB50 revealed considerable thermostability, retaining over 75% activity after 1-h incubation at 50 °C. Considering the thermal properties of agar, this makes these enzymes promising candidates for industrial processing.

Tailoring Particle-Enzyme Nanoconjugates for Biocatalysis at the Organic-Organic Interface.

Nonaqueous Pickering emulsions (PEs) are a powerful platform for catalysis design, offering both a large interface contact and a preferable environment for water-sensitive synthesis. However, up to now, little progress has been made to incorporate insoluble enzymes into the nonaqueous system for biotransformation. Herein, we present biocatalytically active nonaqueous PEs, stabilized by particle-enzyme nanoconjugates, for the fast transesterification and esterification, and eventually for biodiesel synthesis. Our nanoconjugates are the hybrid biocatalysts tailor-made by loading hydrophilic Candida antarctica lipase B onto hydrophobic silica nanoparticles, resulting in not only catalytically active but highly amphiphilic particles for stabilization of a methanol-decane emulsion. The enzyme activity in these PEs is significantly enhanced, ca. 375-fold higher than in the nonaqueous biphasic control. Moreover, the PEs can be multiply reused without significant loss of enzyme performance. With this proof-of-concept, this system can be expanded for many advanced syntheses using different enzymes in the future.

Biodegradation of Ephedrine Isomers by Arthrobacter sp. Strain TS-15: Discovery of Novel Ephedrine and Pseudoephedrine Dehydrogenases.

The Gram-positive soil bacterium Arthrobacter sp. strain TS-15 (DSM 32400), which is capable of metabolizing ephedrine as a sole source of carbon and energy, was isolated. According to 16S rRNA gene sequences and comparative genomic analysis, Arthrobacter sp. TS-15 is closely related to Arthrobacter aurescens Distinct from all known physiological paths, ephedrine metabolism by Arthrobacter sp. TS-15 is initiated by the selective oxidation of the hydroxyl function at the α-C atom, yielding methcathinone as the primary degradation product. Rational genome mining revealed a gene cluster potentially encoding the novel pathway. Two genes from the cluster, which encoded putative short-chain dehydrogenases, were cloned and expressed in Escherichia coli The obtained enzymes were strictly NAD+ dependent and catalyzed the oxidation of ephedrine to methcathinone. Pseudoephedrine dehydrogenase (PseDH) selectively converted (S,S)-(+)-pseudoephedrine and (S,R)-(+)-ephedrine to (S)- and (R)-methcathinone, respectively. Ephedrine dehydrogenase (EDH) exhibited strict selectivity for the oxidation of the diastereomers (R,S)-(-)-ephedrine and (R,R)-(-)-pseudoephedrine.IMPORTANCEArthrobacter sp. TS-15 is a newly isolated bacterium with the unique ability to degrade ephedrine isomers. The initiating steps of the novel metabolic pathway are described. Arthrobacter sp. TS-15 and its isolated ephedrine-oxidizing enzymes have potential for use in decontamination and synthetic applications.

Living whole-cell catalysis in compartmentalized emulsion.

Whole-cell biocatalysis plays an important role in biotransformation with unique features such as good tolerance of solvents and easy recycling. However, the relatively low catalytic efficiency limits their use in real production. In this study, a multi-compartmentalized emulsion in organic solvent was constructed to encapsulate living cells for enhanced catalytic performance. Extraordinary large interfacial area of the emulsion improved the bioactivity of Escherichia coli (E. Coli) cells up to 137 times compared to a standard biphasic system. The emulsion was stabilized by a biocompatible polymer and prepared by gentle shaking by hand, which resulted in good cell viability. Moreover, the encapsulated cells could be easily recycled, and the activity remained more than 70% after five cycles. This work provides a promising approach for utilizing whole-cell catalysts for efficient organic catalysis.

Efficient and Selective Carboligation with Whole-Cell Biocatalysts in Pickering Emulsion.

Pickering emulsions (PEs) are particle-stabilized multiphase systems with promising features for synthetic applications. Described here is a novel, simplified set-up employing catalytically active whole cells for simultaneous emulsion stabilization and synthetic reaction. In the stereoselective carboligation of benzaldehyde to (R)-benzoin catalyzed by a benzaldehyde lyase in E. coli, the set-up yielded maximum substrate conversion within very short time, while economizing material demand and waste. Formation and activity of freshly produced PEs were enhanced when the catalytic whole cells were covered with hydrophobic silicone prior to PE formation. Benchmarked against other easy-to-handle whole-cell biocatalysts in pure organic solvent, neat substrate, an aqueous emulsion in substrate, and a micro-aquatic system, respectively, the cell-stabilized PE outperformed all other systems by far.

Heterogeneous Metal-Organic-Framework-Based Biohybrid Catalysts for Cascade Reactions in Organic Solvent.

In cooperative catalysis, the combination of chemo- and biocatalysts to perform one-pot reactions is a powerful tool for the improvement of chemical synthesis. Herein, UiO-66-NH2 was employed to stepwise immobilize Pd nanoparticles (NPs) and Candida antarctica lipase B (CalB) for the fabrication of biohybrid catalysts for cascade reactions. Distinct from traditional materials, UiO-66-NH2 has a robust but tunable structure that can be utilized with a ligand exchange approach to adjust its hydrophobicity, resulting in excellent catalyst dispersity in diverse reaction media. These attractive properties contribute to the formation of MOF-based biohybrid catalysts with high activity and selectivity in the synthesis of benzyl hexanoate from benzaldehyde and ethyl hexanoate. With this proof-of-concept, we reasonably expect that future tailor-made MOFs can combine other catalysts, ranging from chemical to biological catalysts for applications in industry.

Compartmentalized Aqueous-Organic Emulsion for Efficient Biocatalysis.

The design and construction of polymeric compartmentalized structures in water have been intensively explored for controllable catalysis, but there is still the challenge of setting up catalytic compartments in organic media. Here, we designed a simple block copolymer, PCL-b-PEG-b-PCL, to construct a stable and multi-compartmentalized emulsion in an organic solvent by hand-shaking. This gentle emulsion preparation allowed a successful encapsulation of vulnerable biocatalysts such as benzaldehyde lyase (BAL) and alcohol dehydrogenase (ADH). The compartmentalization provided the emulsion with an exceptionally large interfacial area that could enhance BAL activity up to 225 times as compared to the traditional biphasic system. Moreover, the system could be easily scaled up due to its facile preparation with low cost. Therefore, our results pave the way for developing compartmentalized structures in solvents for biocatalysis in large-scale synthetic chemistry.

Ultralong-Discharge-Time Biobattery Based on Immobilized Enzymes in Bilayer Rolled-Up Enzymatic Nanomembranes.

Glucose biofuel cells (GBFCs) are highly promising power sources for implantable biomedical and consumer electronics because they provide a high energy density and safety. However, it remains a great challenge to combine their high power density with reliable long-term stability. In this study, a novel GBFC design based on the enzyme biocatalysts glucose dehydrogenase, diaphorase, and bilirubin oxidase immobilized in rolled-up titanium nanomembranes is reported. The setup delivers a maximum areal power density of ≈3.7 mW cm-2 and a stable power output of ≈0.8 mW cm-2 . The power discharges over 452 h, which is considerably longer than reported previously. These results demonstrate that the GBFC design is in principle a feasible and effective approach to solve the long-term discharge challenge for implantable biomedical device applications.

Progress in biocatalysis with immobilized viable whole cells: systems development, reaction engineering and applications.

Viable microbial cells are important biocatalysts in the production of fine chemicals and biofuels, in environmental applications and also in emerging applications such as biosensors or medicine. Their increasing significance is driven mainly by the intensive development of high performance recombinant strains supplying multienzyme cascade reaction pathways, and by advances in preservation of the native state and stability of whole-cell biocatalysts throughout their application. In many cases, the stability and performance of whole-cell biocatalysts can be highly improved by controlled immobilization techniques. This review summarizes the current progress in the development of immobilized whole-cell biocatalysts, the immobilization methods as well as in the bioreaction engineering aspects and economical aspects of their biocatalytic applications.

Scalable preparation of silCoat-biocatalysts by use of a fluidized-bed reactor.

SilCoat-biocatalysts are immobilized enzyme preparations with an outstanding robustness against leaching and mechanical stress and therefore promising tools for technical synthesis. They consist of a composite material made from a solid enzyme carrier and silicone. In this study, a method has been found to enable provision of these catalysts in large scale. It makes use of easily scalable fluidized-bed technology and, in contrast to the original method, works in almost complete absence of organic solvent. Thus, it is both a fast and safe method. When the Pt-catalyst required for silicone formation is cast on the solid enzyme carrier before coating, resulting composites resemble the original preparations in morphology, catalytic activity, and stability against leaching and mechanical forces. Only the maximum total content of silicone in the composites lies about 10% w/w lower resulting in an overall leaching stability below the theoretical maximum. When the Pt-catalyst is mixed with cooled siloxane solution before coating, surficial coating of the enzyme carriers is achieved, which provides maximum leaching stability at very low silicone consumption. Thus, the technology offers the possibility to produce both composite and for the first time also core-shell silCoat-particles, and optimize leaching stability over mechanical strength according to process requirements.

A continuous single organic phase process for the lipase catalyzed synthesis of peroxy acids increases productivity.

The design of an optimal process is particularly crucial when the reactants deactivate the biocatalyst. The reaction cascades of the chemo-enzymatic epoxidation where the intermediate peroxy acid is produced by an enzyme are still limited by enzyme inhibition and deactivation by hydrogen peroxide. To avoid additional effects caused by interfaces (aq/org) and to reduce the process limiting deactivation by the substrate hydrogen peroxide, a single-phase concept was applied in a fed-batch and a continuous process (stirred tank), without the commonly applied addition of a carrier solvent. The synthesis of peroxyoctanoic acid catalyzed by Candida antarctica lipase B was chosen as the model reaction. Here, the feasibility of this biocatalytic reaction in a single-phase system was shown for the first time. The work shows the economic superiority of the continuous process compared to the fed-batch process. Employing the fed-batch process reaction rates up to 36 mmol h-1 per gramcat, and a maximum yield of 96 % was achieved, but activity dropped quickly. In contrast, continuous operation can maintain long-term enzyme activity. For the first time, the continuous enzymatic reaction could be performed for 55 h without any loss of activity and with a space-time yield of 154 mmol L-1 h-1, which is three times higher than in the fed-batch process. The higher catalytic productivity compared to the fed-batch process (34 vs. 18 gProd g-1 cat) shows the increased enzyme stability in the continuous process.

Activity prediction of substrates in NADH-dependent carbonyl reductase by docking requires catalytic constraints and charge parameterization of catalytic zinc environment.

Molecular docking of substrates is more challenging compared to inhibitors as the reaction mechanism has to be considered. This becomes more pronounced for zinc-dependent enzymes since the coordination state of the catalytic zinc ion is of greater importance. In order to develop a predictive substrate docking protocol, we have performed molecular docking studies of diketone substrates using the catalytic state of carbonyl reductase 2 from Candida parapsilosis (CPCR2). Different docking protocols using two docking methods (AutoDock Vina and AutoDock4.2) with two different sets of atomic charges (AM1-BCC and HF-RESP) for catalytic zinc environment and substrates as well as two sets of vdW parameters for zinc ion were examined. We have selected the catalytic binding pose of each substrate by applying mechanism based distance criteria. To compare the performance of the docking protocols, the correlation plots for the binding energies of these catalytic poses were obtained against experimental Vmax values of the 11 diketone substrates for CPCR2. The best correlation of 0.73 was achieved with AutoDock4.2 while treating catalytic zinc ion in optimized non-bonded (NBopt) state with +1.01 charge on the zinc ion, compared to 0.36 in non-bonded (+2.00 charge on the zinc ion) state. These results indicate the importance of catalytic constraints and charge parameterization of catalytic zinc environment for the prediction of substrate activity in zinc-dependent enzymes by molecular docking. The developed predictive docking protocol described here is in principle generally applicable for the efficient in silico substrate spectra characterization of zinc-dependent ADH.

Investigation of Structural Determinants for the Substrate Specificity in the Zinc-Dependent Alcohol Dehydrogenase CPCR2 from Candida parapsilosis.

Zinc-dependent alcohol dehydrogenases (ADHs) are a class of enzymes applied in different biocatalytic processes ranging from lab to industrial scale. However, one drawback is the limited substrate range, necessitating a whole array of different ADHs for the relevant substrate classes. In this study, we investigated structural determinants of the substrate spectrum in the zinc-dependent ADH carbonyl reductase 2 from Candida parapsilosis (CPCR2), combining methods of mutational analysis with in silico substrate docking. Assigned active site residues were genetically randomized, and the resulting mutant libraries were screened with a selection of challenging carbonyl substrates. Three variants (C57A, W116K, and L119M) with improved activities toward different substrates were detected at neighboring positions in the active site. Thus, all possible combinations of the mutations were generated and characterized for their substrate specificity, yielding several improved variants. The most interesting were a C57A variant, with a 27-fold increase in specific activity for 4'-acetamidoacetophenone, and the double mutant CPCR2 B16-(C57A, L119M), with a 45-fold improvement in the kcat ⋅KM (-1) value. The obtained variants were further investigated by in silico docking experiments. The results indicate that the mentioned residues are structural determinants of the substrate specificity of CPCR2, being major players in the definition of the active site. Comparison of these results with closely related enzymes suggests that these might even be transferred to other ADHs.

Enzymatically cross-linked hyperbranched polyglycerol hydrogels as scaffolds for living cells.

Although several strategies are now available to enzymatically cross-link linear polymers to hydrogels for biomedical use, little progress has been reported on the use of dendritic polymers for the same purpose. Herein, we demonstrate that horseradish peroxidase (HRP) successfully catalyzes the oxidative cross-linking of a hyperbranched polyglycerol (hPG) functionalized with phenol groups to hydrogels. The tunable cross-linking results in adjustable hydrogel properties. Because the obtained materials are cytocompatible, they have great potential for encapsulating living cells for regenerative therapy. The gel formation can be triggered by glucose and controlled well under various environmental conditions.