Increase In Turnover Number Research Articles

Enabling High Activation of Glucose-6-Phosphate Dehydrogenase Activity Through Liquid Condensate Formation and Compression.

Droplet formation via liquid-liquid phase separation is thought to be involved in the regulation of various biological processes, including enzymatic reactions. We investigated a glycolytic enzymatic reaction, the conversion of glucose-6-phosphate to 6-phospho-D-glucono-1,5-lactone with concomitant reduction of NADP+ to NADPH both in the absence and presence of dynamically controlled liquid droplet formation. Here, the nucleotide serves as substrate as well as the scaffold required for the formation of liquid droplets. To further expand the process parameter space, temperature and pressure dependent measurements were performed. Incorporation of the reactants in the liquid droplet phase led to a boost in enzymatic activity, which was most pronounced at medium-high pressures. The crowded environment of the droplet phase induced a marked increase of the affinity of the enzyme and substrate. An increase in turnover number in the droplet phase at high pressure contributed to a further strong increase in catalytic efficiency. Enzyme systems that are dynamically coupled to liquid condensate formation may be the key to deciphering many biochemical reactions. Expanding the process parameter space by adjusting temperature and pressure conditions can be a means to further increase the efficiency of industrial enzyme utilization and help uncover regulatory mechanisms adopted by extremophiles.

Boosting Visible‐Light Carbon Dioxide Reduction with Imidazolium‐Based Ionic Liquids

AbstractEfficiently generating C1 building blocks from environmentally friendly carbon sources, such as through photocatalytic CO2 reduction, is essential for fostering a sustainable circular economy. The pursuit of mild catalytic activation methods has yielded powerful catalysts that can be synergistically employed alongside various reaction media to enhance overall performance. Herein, we elucidate the influence of diverse imidazolium‐based ionic liquids as additives for visible‐light‐driven CO2 reduction with ruthenium(II)‐ and rhenium(I)‐bipyridine complexes. Our investigation reveals that incorporating ionic liquids into traditional solvents at concentrations below 10 % can markedly boost CO production while suppressing H2 generation. The best results were obtained for the highly basic ionic liquid [C2mim][OAc], resulting in a substantial rise in CO formation from 0.3 μmol/h to 5.4 μmol/h and an increase in turnover number from 3 to 59. This study underscores the cooperative influence of imidazolium‐based ionic liquids on CO2 photoreduction while circumventing their use as primary solvents, thus offering a promising avenue for sustainable chemical synthesis.

Theoretical Improvements in Enzyme Efficiency Associated with Noisy Rate Constants and Increased Dissipation.

Previous studies have revealed the extraordinarily large catalytic efficiency of some enzymes. High catalytic proficiency is an essential accomplishment of biological evolution. Natural selection led to the increased turnover number, kcat, and enzyme efficiency, kcat/KM, of uni-uni enzymes, which convert a single substrate into a single product. We added or multiplied random noise with chosen rate constants to explore the correlation between dissipation and catalytic efficiency for ten enzymes: beta-galactosidase, glucose isomerase, β-lactamases from three bacterial strains, ketosteroid isomerase, triosephosphate isomerase, and carbonic anhydrase I, II, and T200H. Our results highlight the role of biological evolution in accelerating thermodynamic evolution. The catalytic performance of these enzymes is proportional to overall entropy production-the main parameter from irreversible thermodynamics. That parameter is also proportional to the evolutionary distance of β-lactamases PC1, RTEM, and Lac-1 when natural or artificial evolution produces the optimal or maximal possible catalytic efficiency. De novo enzyme design and attempts to speed up the rate-limiting catalytic steps may profit from the described connection between kinetics and thermodynamics.

Single-site modification of the P450-BM3 substrate-entrance facilitates the synthesis of optically pure pharmaceutically useful methyl trans-3-phenylglycidates

Optically pure methyl trans-3-phenylglycidates are useful chiral blocks or intermediates in the pharmaceutic field. However, high efficiency and enantioselective synthetic methods remain to be developed. We report an enzymatic process, based on rationally modifying the site D68 at the entrance of the P450-BM3 monooxygenase, thereby creating a mutant D68V with high epoxidation activity and high stereoselectivity toward methyl cinnamate as a cheap substrate. About 9-fold increase in turnover number compared to the wild type was achieved. Furthermore, with molecular dynamics simulations, the reasons for increased activity and stereoselectivity were unveiled. The best mutant also presents high activity toward methyl cinnamate analogs with fluorinated benzyl group. All epoxy products were produced on a gram-scale by whole-cells catalysis. In addition, a series of (+)-prebalamide derivatives were chemically synthesized from these products. This work not only expands the biocatalytic toolbox for producing methyl trans-3-phenylglycidates, but also identifies a new hotspot for engineering P450-BM3.

Catalytic Hydrogenation of CO2 to Formate Using Ruthenium Nanoparticles Immobilized on Supported Ionic Liquid Phases.

Ruthenium nanoparticles (NPs) immobilized on imidazolium-based supported ionic liquid phases (Ru@SILP) act as effective heterogeneous catalysts for the hydrogenation of carbon dioxide (CO2 ) to formate in a mixture of water and triethylamine (NEt3 ). The structure of the imidazolium-based molecular modifiers is varied systematically regarding side chain functionality (neutral, basic, and acidic) and anion to assess the influence of the IL-type environment on the NPs synthesis and catalytic properties. The resulting Ru@SILP materials contain well-dispersed Ru NPs with diameters in the range 0.8-2.9nm that are found 2 to 10 times more active for CO2 hydrogenation than a reference Ru@SiO2 catalyst under identical conditions. Introduction of sulfonic acid groups in the IL modifiers results in a greatly increased turnover number (TON) and turnover frequency (TOF) at reduced metal loadings. As a result, excellent productivity with TONs up to 16100 at an initial TOF of 1430 h-1 can be achieved with the Ru@SILP(SO3 H-OAc) catalyst. H/D exchange and other control experiments suggest an accelerated desorption of the formate species from the Ru NPs promoted by the presence of ammonium sulfonate species on Ru@SILP(SO3 H-X) materials, resulting in enhanced catalyst activity and productivity.

Mechanism‐Guided Computational Design of ω‐Transaminase by Reprograming of High‐Energy‐Barrier Steps

Abstractω‐Transaminases (ω‐TAs) show considerable potential for the synthesis of chiral amines. However, their low catalytic efficiency towards bulky substrates limits their application, and complicated catalytic mechanisms prevent precise enzyme design. Herein, we address this challenge using a mechanism‐guided computational enzyme design strategy by reprograming the transition and ground states in key reaction steps. The common features among the three high‐energy‐barrier steps responsible for the low catalytic efficiency were revealed using quantum mechanics (QM). Five key residues were simultaneously tailored to stabilize the rate‐limiting transition state with the aid of the Rosetta design. The 14 top‐ranked variants showed 16.9–143‐fold improved catalytic activity. The catalytic efficiency of the best variant, M9 (Q25F/M60W/W64F/I266A), was significantly increased, with a 1660‐fold increase in kcat/Km and a 1.5–26.8‐fold increase in turnover number (TON) towards various indanone derivatives.

Mechanism-Guided Computational Design of ω-Transaminase by Reprograming of High-Energy-Barrier Steps.

ω-Transaminases (ω-TAs) show considerable potential for the synthesis of chiral amines. However, their low catalytic efficiency towards bulky substrates limits their application, and complicated catalytic mechanisms prevent precise enzyme design. Herein, we address this challenge using a mechanism-guided computational enzyme design strategy by reprograming the transition and ground states in key reaction steps. The common features among the three high-energy-barrier steps responsible for the low catalytic efficiency were revealed using quantum mechanics (QM). Five key residues were simultaneously tailored to stabilize the rate-limiting transition state with the aid of the Rosetta design. The 14 top-ranked variants showed 16.9-143-fold improved catalytic activity. The catalytic efficiency of the best variant, M9 (Q25F/M60W/W64F/I266A), was significantly increased, with a 1660-fold increase in kcat /Km and a 1.5-26.8-fold increase in turnover number (TON) towards various indanone derivatives.

Continuous‐Flow Dynamic Kinetic Resolution of Racemic Alcohols by Lipase–Oxovanadium Cocatalysis

A continuous‐flow dynamic kinetic resolution of racemic secondary alcohols was carried out using a single column reactor packed with a mixture of immobilized lipase and an immobilized oxovanadium species, VMPS4. As a result, optically pure esters were produced in 88–92 % yields. Problems encountered in this study were overcome by using fillers that efficiently maintained the initial distribution of the catalysts in the reactor and by using a packing method in which the mixing ratio of the two catalysts was varied in a stepwise fashion. The flow process led to an increased turnover number of each catalyst compared to those of batch reactions.

Engineering of a highly thermostable endoglucanase from the GH7 family of Bipolaris sorokiniana for higher catalytic efficiency.

In a previous study, we reported an alkaliphilic and thermostable endoglucanase (BsGH7-3) of glycoside hydrolase family 7 (GH7) from the hemibiotrophic plant pathogen Bipolaris sorokiniana. However, the catalytic efficiency of the enzyme was lower than for some other endoglucanases of the GH7 family reported in the literature. To engineer a more active enzyme, we identified conserved residues in the substrate-binding tunnel and on the surface of the protein that could play a role in charge-charge interaction and stabilize the structure. The mutants D257W and Q225H in the substrate-binding tunnel and Y222R and Q401N on the protein surface showed a 2-fold increase in specific activity and a 1.5-fold increase in turnover number and were active over a broader range of pH. The mutants also showed a higher tolerance to NaCl. The rational design of the BsGH7-3 mutants helped in increasing the catalytic efficiency of the thermostable enzyme and may be useful in combination with other cellulases like cellobiohydrolase and β-glucosidase towards complete saccharification of cellulose into glucose.

Orthogonal Supramolecular Assembly Triggered by Inclusion and Exclusion Interactions with Cucurbit[7]uril for Photocatalytic H2 Evolution.

The fabrication of efficient and convenient photocatalytic H2 evolution systems is a fascinating research topic in the field of solar energy conversion. A ternary self-assembled photocatalytic H2 evolution system was fabricated through supramolecular host-guest chemistry. The system consisted of the H2 evolution catalyst [Co(dmgH)2 (4-ppy)2 ]NO3 (1; dmgH2 =dimethylglyoxime, 4-ppy=4-phenylpyridine) and the photosensitizer Eosin Y (EY) assembled with the macrocyclic compound cucurbit[7]uril (CB[7]) to form the 1@CB[7]/EY complex through inclusion and exclusion interactions, respectively. The synchronous self-assembly drives an orthogonal arrangement of the 1@CB[7]/EY system. The inclusion complex 1@CB[7] was successfully characterized by 1 H NMR spectroscopy and single-crystal XRD. The exclusion process of CB[7] with EY was identified by NMR titration and the optimized geometry of the exclusion structure was determined by DFT calculations. The use of CB[7] resulted in a 6-fold increase in turnover number, a 3-fold increase in turnover frequency, and a 3-fold extension of lifetime for photocatalytic H2 evolution as compared with the system in the absence of CB[7]. The improvement of the light-driven H2 evolution activity was ascribed to the ability of CB[7] to link the photosensitizer and catalyst.

Improving Photocatalysis for the Reduction of CO2 through Non-covalent Supramolecular Assembly.

We report the enhancement of photocatalytic performance by introduction of hydrogen-bonding interactions to a Re bipyridine catalyst and Ru photosensitizer system (ReDAC/RuDAC) by the addition of amide substituents, with carbon monoxide (CO) and carbonate/bicarbonate as products. This system demonstrates a more-than-3-fold increase in turnover number (TONCO = 100 ± 4) and quantum yield (ΦCO = 23.3 ± 0.8%) for CO formation compared to the control system using unsubstituted Ru photosensitizer (RuBPY) and ReDAC (TONCO = 28 ± 4 and ΦCO = 7 ± 1%) in acetonitrile (MeCN) with 1,3-dimethyl-2-phenyl-2,3-dihydro-1H-benzo[d]imidazole (BIH) as sacrificial reductant. In dimethylformamide (DMF), a solvent that disrupts hydrogen bonds, the ReDAC/RuDAC system showed a decrease in catalytic performance while the control system exhibited an increase, indicating the role of hydrogen bonding in enhancing the photocatalysis for CO2 reduction through supramolecular assembly. The similar properties of RuDAC and RuBPY demonstrated in lifetime measurements, spectroscopic analysis, and electrochemical and spectroelectrochemical studies revealed that the enhancement in photocatalysis is due not to differences in intrinsic properties of the catalyst or photosensitizer, but to hydrogen-bonding interactions between them.

Nanoporous Zeolite-X as a new carrier for laccase immobilization and its application in dyes decolorization

Abstract Laccase enzyme from Polyporus durus ATCC 26726 was immobilized on nanoporous Zeolite-X (ZX), with 83% immobilization yield. The immobilization process protected laccase against pH and temperature changes. The activation energy was lowered after immobilization. Compared to the free enzyme the immobilized enzyme displayed higher Km value and lower Vmax. The immobilized laccase exhibited higher half-life values (t1/2), higher decimal reduction time (D-value) and lower deactivation rate constant (Kd) within the temperature range of 50–70 °C. The thermodynamic analysis for substrate oxidation indicated that the enthalpy (ΔH*), entropy (ΔS*), and free energy of transition state (ΔG*E–T) were lower for immobilized laccase. Furthermore, there was an increase in turnover number (kcat) after immobilization. The immobilized laccase could decolorize two dyes and two synthetic wastewater solutions. It retained 100% activity against AB 225 dye after 7 successive decolorization cycles and it could be reused for 11 times with 48% activity loss.

Palladium-mediated hybrid biocatalysts with enhanced enzymatic catalytic performance via allosteric effects

High activity and stability of immobilized enzymes have been constant pursuits and critical challenges for decades. Herein, Cytochrome c (peroxidase, Cyt c) and its corresponding enzyme mimic (Pd nanoparticles) were combined and successfully embedded into a zeolitic imidazolate framework-8 (ZIF-8) to enhance the enzymatic catalytic performance using a biomimetic mineralization approach. Owing to allosteric effects of Cyt c-Pd complexes, the as-synthesized Cyt c-Pd@ZIF-8 composites exhibit an increased turnover number (approximately 2.4-fold for kcat) and an enhanced catalytic efficiency (approximately 2.3-fold for kcat/KM) compared to free Cyt c; also the shielding effect of ZIF-8 endows enzyme with improved resistance against harsh conditions (e.g. high temperatures and organic solvents). The strategy, which integrates enzyme with its enzyme mimic derived from transition metal nanoparticles to enhance enzymatic catalytic performances, may provide a versatile and facile technique for designing highly efficient and multi-functional bio-catalysts.

Engineering Bacillus pumilus alkaline serine protease to increase its low-temperature proteolytic activity by directed evolution

BackgroundMesophilic alkaline serine proteases from various bacteria have been commercially applied in a range of industries owing to their high catalytic efficiency and wide substrate specificity. However, these proteases have an optimal catalytic temperature of approximately 50 °C, and their activity decreases significantly at low temperature. Therefore, to enhance their cold activity, it is necessary to improve the catalytic performance of these proteases at low temperature. The alkaline serine protease (DHAP) from Bacillus pumilus BA06 is a typical mesophilic enzyme, which has demonstrated great potential in various industrial applications. Here we attempted to improve the cold activity of DHAP via directed evolution.ResultsSeven variants (P9S, A1G/K27Q, A38V, A116T, T162I, S182R, and T243S) of DHAP from B. pumilus were obtained via directed evolution. The results showed that all of the variants had increased proteolytic activity at 15 °C towards both the casein and synthetic peptide substrates. With the exception of variant T243S, the thermostability of these variants did not decrease in comparison with the wild-type enzyme. Kinetic analysis indicated that the increase in catalytic efficiency was largely attributed to the increase in turnover number (kcat). Furthermore, the combined variants generated by site-directed mutagenesis showed a further increase in specific caseinolytic activity and the kcat value for hydrolysis of the synthetic peptide. The combined variants of P9S/K27Q and P9S/T162I exhibited an approximate 5-fold increase in caseinolytic activity at 15 °C and almost no loss of thermostability. Finally, the possible mechanism responsible for the change in catalytic properties for these variants was interpreted based on structural modeling.ConclusionsDirected evolution and site-directed mutagenesis were combined to engineer variants of the DHAP from B. pumilus. All of the variants exhibited an increase in hydrolytic efficiency at low temperature towards both of the substrates, casein and synthetic peptide, without any loss of thermostability compared with the wild-type. These data suggest that engineering low-temperature activity for a bacterial protease is not always associated with the loss of thermostability. Furthermore, our findings demonstrate that enhanced cold activity and thermostability could be integrated into a single variant.

Pore Environment Effects on Catalytic Cyclohexane Oxidation in Expanded Fe2(dobdc) Analogues

Metal-organic frameworks are a new class of heterogeneous catalysts in which molecular-level control over both the immediate and long-range chemical environment surrounding a catalytic center can be readily achieved. Here, the oxidation of cyclohexane to cyclohexanol and cyclohexanone is used as a model reaction to investigate the effect of a hydrophobic pore environment on product selectivity and catalyst stability in a series of iron-based frameworks. Specifically, expanded analogues of Fe2(dobdc) (dobdc4- = 2,5-dioxido-1,4-benzenedicarboxylate) were synthesized and evaluated, including the biphenyl derivative Fe2(dobpdc) (H4dobpdc = 4,4'-dihydroxy-[1,1'-biphenyl]-3,3'-dicarboxylic acid), the terphenyl derivative Fe2(dotpdc) (H4dotpdc = 4,4″-dihydroxy-[1,1':4',1″-terphenyl]-3,3″-dicarboxylic acid), and three modified terphenyl derivatives in which the central ring is replaced with tetrafluoro-, tetramethyl-, or di-tert-butylaryl groups. Within these five materials, a remarkable 3-fold enhancement of the alcohol:ketone (A:K) ratio and an order of magnitude increase in turnover number are achieved by simply altering the framework pore diameter and installing nonpolar functional groups near the iron site. Mössbauer spectroscopy, kinetic isotope effect, and gas adsorption measurements reveal that variations in the A:K selectivities arise from differences in the cyclohexane adsorption enthalpies of these frameworks, which become more favorable as the number of hydrophobic residues and thus van der Waals interactions increase.

Differential effect of a chemical denaturant on activity and stability of a serine protease in nonaqueous media

With reference to industrial application, reusability of the biocatalyst is an important criterion which determines the cost of the final product. Urea-induced structural perturbation of proteases has led to higher enzymatic activity, especially in nonaqueous media. The mechanism behind this phenomenon has not been investigated in detail. Using the transesterification activity of subtilisin Carlsberg in nonaqueous media as an illustration, we report that the higher activity is due to simultaneous decrease in Michaelis constant and increase in turnover number of the enzyme. However, we show that this perturbed architecture is unable to retain the high activity-conformation for further rounds of catalysis. Thus, we conclude that the use of an enzyme for commercial applications is dependent upon a compromise between activity and (operational) stability.

Improving singlet oxygen resistance during photochemical water oxidation by cobalt porphyrin catalysts.

Enabling the production of solar fuels on a global scale through artificial photosynthesis requires the development of water oxidation catalysts with significantly improved stability. The stability of photosystems is often reduced owing to attack by singlet oxygen, which is produced during light harvesting. Here, we report photochemical water oxidation by CoFPS, a fluorinated Co-porphyrin designed to resist attack by singlet oxygen. CoFPS exhibits significantly improved stability relative to its non-fluorinated analogue, as shown by a large increase in turnover numbers. This increased stability results from resistance of CoFPS to attack by singlet oxygen, the formation of which was monitored in situ by using 9,10-diphenylanthracene as a chemical probe. Dynamic light scattering (DLS) confirms that CoFPS remains homogeneous, proving its stability during water oxidation catalysis.

Enhanced catalytic efficiency in quercetin-4'-glucoside hydrolysis of Thermotoga maritima β-glucosidase A by site-directed mutagenesis.

Te-BglA and Tm-BglA are glycoside hydrolase family 1 β-glucosidases from Thermoanaerobacter ethanolicus JW200 and Thermotoga maritima, respectively, with 53% sequence identity. However, Te-BglA could more effectively hydrolyze isoflavone glucosides to their aglycones than could Tm-BglA, possibly due to the difference in amino acid residues around their glycone binding pockets. Site-directed mutagenesis was used to replace the amino acid residues of Tm-BglA with the corresponding residues of Te-BglA, generating three single mutants (F221L, N223L, and G224T), as well as the corresponding three double mutants (F221L/N223L, F221L/G224T, and N223L/G224T) and one triple mutant (F221L/N223L/G224T). The seven mutants have been purified, characterized, and compared to the wild-type Tm-BglA. The effects of the mutations on kinetics, enzyme activity, and substrate specificity were determined. All mutants showed pH-activity curves narrower on the basic side and wider on the acid side and had similar optimal pH and stability at pH 6.5-8.3. They were more stable up to 85 °C, but G224T displayed higher optimal temperature than Tm-BglA. Seven mutants indicated an obvious increase in catalytic efficiency toward p-nitrophenyl β-D-glucopyranoside (pNPG) but an increase or not change in K(m). All mutants showed a decrease in catalytic efficiency of isoflavonoid glycosides and were not changed for F221L and lost for N223L in enzymatic hydrolysis on quercetin glucosides. Contrarily, G224T resulted in a dramatic increase conversion of Q4' (35.5%) and Q3,4' (28.6%) in accord with an increased turnover number (k(cat), 1.4×) and catalytic efficiency (k(cat)/K(m), 2.2×) as well as a decrease in K(m) (0.24) for Q4'. Modeling showed that G224T mutation at position 224 may enhance the interaction between G224T and 5-OH and 3-OH on the quercetin backbone of Q4'.

Substrate scope and selectivity in offspring to an enzyme subjected to directed evolution

We have analyzed the effects of mutations inserted during directed evolution of a specialized enzyme, Escherichiacoli S-1,2-propanediol oxidoreductase (FucO). The kinetic properties of evolved variants have been determined and the observed differences have been rationalized by modeling the tertiary structures of isolated variants and the wild-type enzyme. The native substrate, S-1,2-propanediol, as well as phenylacetaldehyde and 2S-3-phenylpropane-1,2-diol, which are new substrates accepted by isolated variants, were docked into the active sites. The study provides a comprehensive picture of how acquired catalytic properties have arisen via an intermediate generalist enzyme, which had acquired a single mutation (L259V) in the active site. Further mutagenesis of this generalist resulted in a new specialist catalyst. We have also been able to relate the native enzyme activities to the evolved ones and linked the differences to individual amino acid residues important for activity and selectivity. F254 plays a dual role in the enzyme function. First, mutation of F254 into an isoleucine weakens the interactions with the coenzyme thereby increasing its dissociation rate from the active site and resulting in a four-fold increase in turnover number with S-1,2-propanediol. Second, F254 is directly involved in binding of aryl-substituted substrates via π-π interactions. On the other hand, N151 is critical in determining the substrate scope since the side chain amide group stabilizes binding of 1,2-substituted diols and is apparently necessary for enzymatic activity with these substrates. Moreover, the side chain of N151 introduces steric hindrance, which prevents high activity with phenylacetaldehyde. Additionally, the hydroxyl group of T149 is required to maintain the catalytically important hydrogen bonding network.

Refolding and Enzyme Kinetic Studies on the Ferrochelatase of the Cyanobacterium Synechocystis sp. PCC 6803

Heme is a cofactor for proteins participating in many important cellular processes, including respiration, oxygen metabolism and oxygen binding. The key enzyme in the heme biosynthesis pathway is ferrochelatase (protohaem ferrolyase, EC 4.99.1.1), which catalyzes the insertion of ferrous iron into protoporphyrin IX. In higher plants, the ferrochelatase enzyme is localized not only in mitochondria, but also in chloroplasts. The plastidic type II ferrochelatase contains a C-terminal chlorophyll a/b (CAB) motif, a conserved hydrophobic stretch homologous to the CAB domain of plant light harvesting proteins and light-harvesting like proteins. This type II ferrochelatase, found in all photosynthetic organisms, is presumed to have evolved from the cyanobacterial ferrochelatase. Here we describe a detailed enzymological study on recombinant, refolded and functionally active type II ferrochelatase (FeCh) from the cyanobacterium Synechocystis sp. PCC 6803. A protocol was developed for the functional refolding and purification of the recombinant enzyme from inclusion bodies, without truncation products or soluble aggregates. The refolded FeCh is active in its monomeric form, however, addition of an N-terminal His6-tag has significant effects on its enzyme kinetics. Strikingly, removal of the C-terminal CAB-domain led to a greatly increased turnover number, kcat, compared to the full length protein. While pigments isolated from photosynthetic membranes decrease the activity of FeCh, direct pigment binding to the CAB domain of FeCh was not evident.