Significant Improvement of Both Catalytic Efficiency and Stability of Fructosyltransferase from Aspergillus niger by Structure-Guided Engineering of Key Residues in the Conserved Sequence of the Catalytic Domain

High level production of a β-fructofuranosidase in Aspergillusniger for the preperation of prebiotic bread using in situ enzymatic conversion

Fructooligosaccharides (FOS) are applied in food, pharmaceutical, and cosmetics. The large scale production of FOS through enzymatic conversion is limited by the expression level and properties of β-fructofuranosidases. A β-fructofuranosidase (AnFTase70) gene from Aspergillus niger was successfully overexpressed in A. niger FBL-B (ΔglaA, ΔamyA, Δaamy, ΔpyrG). The highest β-fructofuranosidase activity of 15,006 U/mL was produced by high-cell density fermentation in a 200 L fermentor, and is so far the highest value ever reported. AnFTase70 was most active at 55 °C and pH 5.5, respectively. It showed high specific activity of 812.0 and 91.8 U/mg towards sucrose and raffinose. AnFTase70 efficiently produced melibiose and FOS with a yield of 55.7 % and 60.6 %, respectively. The membrane filtration system significantly increased the FOS content from 56.1 % to 95.3 % (w/w) with a FOS yield of 69.1 %. Moreover, AnFTase70 was added into bread making to produce a rich prebiotic bread with the highest FOS content of 3.3 g/100 g by in situ enzyme conversion. This study provides a promising way for efficient production of β-fructofuranosidase in A. niger as well as in situ synthesis of FOS in foods.

Improving the hydrophilic microenvironment surrounding the catalytic site of fructosyltransferase enhances its catalytic ability

The hydrophilic microenvironment surrounding an enzyme's active site can influence its catalytic activity. This study examines the effect of enhancing this environment in the Aspergillus niger fructosyltransferase, SucC. Bioinformatics analysis identified a cysteine residue (C66) near the catalytic triad (D64, D194, E271) as vital for maintaining the active site's structure and facilitating substrate transport. Simulated mutagenesis suggested that mutating cysteine to serine (C66S) could increase hydrophilicity without altering the structure significantly. This mutation was predicted to enhance substrate affinity, with binding energy changing from -3.65 to -4.14 kcal mol-1. The C66S mutant, expressed in Pichia pastoris GS115, showed a 61.3% increase in specific activity, a 13.5% decrease in Km (82.20/71.14 mM), and a 21.6% increase in kcat (112.23/136.48 min-1), resulting in a 40.1% increase in catalytic efficiency (1.37/1.92 min-1 mM-1). For fructooligosaccharides (FOS) production, C66S demonstrated enhanced transfructosylation, particularly in the initial stages of the reaction, achieving higher overall FOS yields. These findings highlight that modifying the active site hydrophilicity, without causing major structural changes, is a promising strategy for improving an enzyme's catalytic efficiency.

The Catalytic Mechanism of Key Enzymes Involved in the Synthesis of Ergothioneine in Lentinula edodes

C-S lyase is a crucial enzyme responsible for the formation of sulfur-containing flavor compounds in Lentinula edodes. We investigated the involvement of C-S lyase in the synthesis of ergothioneine (EGT) in L. edodes, a high-producing edible mushroom. Through experimental and computational approaches, we identified Lecsl2, a C-S lyase, as a key enzyme involved in EGT synthesis in L. edodes. We characterized the enzymatic catalytic mechanism of Egt1 and Egt2, the two enzymes primarily catalyzing EGT synthesis in fungi. The results showed that Egt1 interacted with His, SAM, and Cys to form the intermediate product Her-sul, while Egt2, a PLP-dependent enzyme, cleaved the C-S bond on Her-sul to produce EGT. However, our findings suggested that Egt2 in L. edodes might not form a covalent bond with PLP, unlike the previously reported catalytic mechanism of Egt2 involving covalent catalysis. The study provided new insights into the synthesis pathway of EGT in L. edodes and highlighted the need for further investigation into the catalytic mechanism of Egt2 in this species.

Significant enhancement of the thermal stability and catalytic efficiency of transglutaminase in Streptomyces mobaraensis engineered through the novel S. mobaraensis genomic mutant library construction method GHR/Sml

Herein, we developed a novel Streptomyces mobaraensis genomic mutant library construction method, GHR/Sml, to directly and significantly enhance the thermal stability and catalytic efficiency of TGase in the genome of S. mobaraensis. First, 13 key amino acid residues and their mutations for enhanced thermal stability were identified using error-prone PCR and site-directed mutagenesis. Then, the GHR/Sml method was developed to construct a TGase genomic mutant library with 13 mutations. Positive mutants S23Y/Y24N/S250R, S23Y/Y24N/S303K, S23Y/Y24N/K294L, S23Y/Y24N/S199A/R208L, S23Y/Y24N, and S250R were obtained from 1500 total mutants; their half-life values at 50 °C were increased by 9.3-, 9.5-, 8.7-, 9.0-, 6.9-, and 4.8-fold compared with that of TGLD, respectively. Furthermore, the kcat/Km of mutant S23Y/Y24N/S250R increased by 1.25-fold over that of TGLD. The activity of S23Y/Y24N/S250R reached 65.34 U/mL in a 1000-L fermenter, which was the highest activity reported. This novel GHR/Sml method is of great significance for systematically improving properties of additional enzymes in the genome of S. mobaraensis.

Improving the Catalytic Properties of Xylanase from Alteromones Macleadii H35 Through Sequence Analysis

Endo-1,4-β-xylanase is a key xylanolytic enzyme, and our study aimed to enhance the catalytic properties of Alteromones Macleadii xylanase (Xyn ZT-2) through sequence-guided design approach. Analysis of the amino acid sequence revealed highly conserved residues near the active site, with few differences. Introducing various mutations allowed us to modify the enzyme's catalytic performance. Particularly, the A152G mutation led to a 9.8-fold increase in activity and a 23.2-fold increase in catalytic efficiency. Moreover, A152G exhibited an optimal temperature of 65 °C, 20 °C higher than that of Xyn ZT-2, while the T287S mutant showed a 4.9-fold increase in half-life. These results underscore the role of amino acid evolution in shaping xylanase catalysis. Through targeted sequence analysis and a focused mutation library, we effectively improved catalytic performance, providing a straightforward approach for enhancing enzyme efficiency.

Application of molecular dynamics simulation in the field of food enzymes: improving the thermal-stability and catalytic ability

Enzymes can produce high-quality food with low pollution, high function, high acceptability, and medical aid. However, most enzymes, in their native form, do not meet the industrial requirements. Sequence-based and structure-based methods are the two main strategies used for enzyme modification. Molecular Dynamics (MD) simulation is a sufficiently comprehensive technology, from a molecular perspective, which has been widely used for structure information analysis and enzyme modification. In this review, we summarize the progress and development of MD simulation, particularly for software, force fields, and a standard procedure. Subsequently, we review the application of MD simulation in various food enzymes for thermostability and catalytic improvement was reviewed in depth. Finally, the limitations and prospects of MD simulation in food enzyme modification research are discussed. This review highlights the significance of MD simulation and its prospects in food enzyme modification.

Crystal structure of urethanase from Candida parapsilosis and insights into the substrate-binding through in silico mutagenesis and improves the catalytic activity and stability

Ethyl carbamate (EC) is classified as a Class 2A carcinogen, and is present in various fermented foods, posing a threat to human health. Urethanase (EC 3.5.1.75) can catalyze EC to produce ethanol, CO2 and NH3. The urethanase (cpUH) from Candida parapsilosis can hydrolyze EC, but its low affinity and poor stability hinder its application. Here, the structure of cpUH from Candida parapsilosis was determined with a resolution of 2.66 Å. Through sequence alignment and site-directed mutagenesis, it was confirmed that cpUH contained the catalytic triad Ser-cisSer-Lys of the amidase family. Then, the structure-oriented engineering mutant N194V of urethanase was obtained. Its urethanase activity increased by 6.12 %, the catalytic efficiency (kcat/Km) increased by 21.04 %, and the enzyme stability was also enhanced. Modeling and molecular docking analysis showed that the variant N194V changed the number of hydrogen bonds between the substrate and the catalytic residue, resulting in enhanced catalytic ability. MD simulation also demonstrated that the introduction of hydrophobic amino acid Val reduced the RMSD value and increased protein stability. The findings of this study suggest that the N194V variant exhibits significant potential for industrial applications due to its enhanced affinity for substrate binding, improved catalytic efficiency, and increased enzyme stability.

Molecular Dynamics Simulation Reveal the Structure-Activity Relationships of Kainoid Synthases

Kainoid synthases are key enzymes in the biosynthesis of kainoids. Kainoids, as represented by DA and KA, are a class of naturally occurring non-protein amino acids with strong neurotransmitter activity in the mammalian central nervous system. Marine algae kainoid synthases include PnDabC from diatoms, which synthesizes domoic acid (DA), and DsKabC and GfKabC from red algae, which synthesize kainic acid (KA). Elucidation of the catalytic mechanism of kainoid synthases is of great significance for the rational design of better biocatalysts to promote the industrial production of kainoids for use in new drugs. Through modeling, molecular docking, and molecular dynamics simulations, we investigated the conformational dynamics of kainoid synthases. We found that the kainoid synthase complexes showed different stability in the simulation, and the binding and catalytic processes showed significant conformational transformations of kainoid synthase. The residues involved in specific interactions with the substrate contributed to the binding energy throughout the simulation process. Binding energy, the relaxed active pocket, electrostatic potential energy of the active pocket, the number and rotation of aromatic residues interacting with substrates during catalysis, and the number and frequency of hydrogen bonds between the individual functional groups revealed the structure-activity relationships and affected the degree of promiscuity of kainoid synthases. Our research enriches the understanding of the conformational dynamics of kainoid synthases and has potential guiding significance for their rational design.

Structure-guided engineered urethanase from Candida parapsilosis with pH and ethanol tolerance to efficiently degrade ethyl carbamate in Chinese rice wine

Urethane hydrolase can degrade the carcinogen ethyl carbamate (EC) in fermented food, but its stability and activity limit its application. In this study, a mutant G246A and a double mutant N194V/G246A with improved cpUH activity and stability of Candida parapsilosis were obtained by site-directed mutagenesis. The catalytic efficiency (Kcat/Km) of mutant G246A and double mutant N194V/G246A are 1.95 times and 1.88 times higher than that of WT, respectively. In addition, compared with WT, the thermal stability and pH stability of mutant G246A and double mutant N194V/G246A were enhanced. The ability of mutant G246A and double mutant N194V/G246A to degrade EC in rice wine was also stronger than that of WT. The mutation increased the stability of the enzyme, as evidenced by decreased root mean square deviation (RMSD) and increased hydrogen bonds between the enzyme and substrate by molecular dynamics simulation and molecular docking analysis. The molecule modification of new cpUH promotes the industrial process of EC degradation.

Recent developments in the production of prebiotic fructooligosaccharides using fungal fructosyltransferases

Prebiotic nutritional ingredients have received attention due to their health-promoting potential and related uses in the food and nutraceutical industries. Recent times have witnessed an increasing interest in the use of fructooligosaccharides (FOS) as prebiotics and their generation using microbial enzymes. FOS consumption is known to confer health benefits such as protection against colon cancer, improved mineral absorption, lowering effect on serum lipid and cholesterol concentration, antioxidant properties, favourable dietary modulation of the human colonic microbiota, and immuno-modulatory effects. Comparative analysis of molecular models of various fructosyltransferases (FTases) reveals the mechanism of action and interaction of substrate with the active site. Microbial FTases carry out transfructosylation of sucrose into fructooligosaccharides (kestose, nystose, and fructofuranosylnystose), the most predominantly used prebiotic oligosaccharides. Furthermore, FOS has also been used for other purposes, such as low-calorie sweeteners, dietary fibres, and as the substrates for fermentation. This review highlights the occurrence, characteristics, immobilisation, and potential applications of FOS-generating fungal FTases. Production, heterologous expression, molecular characteristics, and modelling of fungal FTases underpinning their biotechnological prospects are also discussed.

Construction of an Escherichia coli cell factory for de novo synthesis of tyrosol through semi-rational design based on phenylpyruvate decarboxylase ARO10 engineering

Tyrosol (2-(4-hydroxyphenyl) ethanol) is extensively used in the pharmaceutical industry as an important natural product from plants. In previous research, we constructed a recombinant Escherichia coli strain capable of de novo synthesis of tyrosol by integrating the phenylpyruvate decarboxylase ARO10 derived from Saccharomyces cerevisiae. Nevertheless, the insufficient catalytic efficiency of ARO10 required the insertion of multiple gene copies into the genome to attain enhanced tyrosol production. In this study, we constructed a mutation library of ARO10 based on a computer-aided semi-rational design strategy and developed a high-throughput screening method for selecting high-yield tyrosol mutants by introducing the heterologous hydroxylase complex HpaBC. Through multiple rounds of screening and site-saturation mutagenesis, we ultimately identified the two optimal ARO10 mutants, ARO10D331V and ARO10D331C, which respectively achieved a tyrosol titer of 2.02 g/L and 2.04 g/L in shake flasks, both representing more than 50 % improvement compared to the wild-type. Our study demonstrates the great potential of computer-based semi-rational enzyme design strategy in metabolic engineering. The high-throughput screening method for target compound derivative possesses a certain level of generality. Ultimately, we obtained promising mutants capable of achieving industrial-scale production of tyrosol, which also lays a solid foundation for the efficient synthesis of tyrosol derivatives.

Structural-guided design to improve the catalytic performance of aldo-keto reductase KdAKR

Aldo-keto reductases (AKRs) are important biocatalysts that can be used to synthesize chiral pharmaceutical alcohols. In this study, the catalytic activity and stereoselectivity of a NADPH-dependent AKR from Kluyveromyces dobzhanskii (KdAKR) toward t-butyl 6-chloro (5S)-hydroxy-3-oxohexanoate ((5S)-CHOH) were improved by mutating its residues in the loop regions around the substrate-binding pocket. And the thermostability of KdAKR was improved by a consensus sequence method targeted on the flexible regions. The best mutant M6 (Y28A/L58I/I63L/G223P/Y296W/W297H) exhibited a 67-fold higher catalytic efficiency compared to the wild-type (WT) KdAKR, and improved R-selectivity toward (5S)-CHOH (dep value from 47.6% to >99.5%). Moreover, M6 exhibited a 6.3-fold increase in half-life (t1/2 ) at 40°C compared to WT. Under the optimal conditions, M6 completely converted 200 g/L (5S)-CHOH to diastereomeric pure t-butyl 6-chloro-(3R, 5S)-dihydroxyhexanoate ((3R, 5S)-CDHH) within 8.0 h, with a space-time yield of 300.7 g/L/day. Our results deepen the understandings of the structure-function relationship of AKRs, providing a certain guidance for the modification of other AKRs.

Molecular dynamics simulations identify the topological weak spots of a protease CN2S8A

Thermophilic enzymes are highly desired in industrial applications due to their efficient catalytic activity at high temperature. However, most enzymes exhibit inferior thermostability and it remains challenging to identify the optimal sites for designing mutations to improve protein stability. To tackle this issue, we integrated topological analysis and all-atom molecular dynamics simulations to efficiently pinpoint the thermally-unstable regions in protein structures. Using a protease CN2S8A as the model, we analyzed the intramolecular hydrogen bonding interactions between adjacent secondary structure elements, and then identified the topological weak spots of CN2S8A where weak hydrogen bonding interactions were formed. To examine the role of these sites in protein structural stability, we designed three virtual mutations at different weak spots and characterized the effects of these mutations on the structural properties of CN2S8A. The results showed that all three mutations increased the protein structural stability. In conclusion, these findings provide a novel method to identify the topological weak spots of proteins, with implications in the rational design of biocatalysts with superior thermostability.

Engineering chitin deacetylase AsCDA for improving the catalytic efficiency towards crystalline chitin

Chitin deacetylase (CDA) catalyzing the deacetylation of crystal chitin is a crucial step in the biosynthesis of chitosan, and also a scientific problem to be solved, which restricts the high-value utilization of chitin resources. This study aims to improve the catalytic efficiency of AsCDA from Acinetobacter schindleri MCDA01 by a semi-rational design using alanine scanning mutagenesis and saturation mutagenesis. The quadruple mutant M11 displayed a 2.31 and 1.73-fold improvement in kcat/Km and specific activity over AsCDA, which can remove 68 % of the acetyl groups from α-chitin. Furthermore, structural analysis suggested that additional hydrogen bonds, contributing the flexibility of amino acids and increasing the negative charge in M11 increased the catalytic efficiency. The microstructure changes of α-chitin pretreated by the mutant M11 were observed and evaluated using ¹³C CP/MAS NMR spectroscopy, FT-IR spectroscopy, XRD and SEM, and the results showed that M11 more efficiently catalyzed the release of acetyl groups from α-chitin. This study would provide a theoretical basis for the molecular modification of CDAs and accelerate the process of industrial production of chitosan by CDAs.

High Production of Maltooligosaccharides in the Starch Liquefaction Process: A Study on the Hyperthermophilic Mechanism of α-Amylase

The efficient production of high-value-added bioproducts from starchy substances requires α-amylases with hyperthermophilic properties for industrial starch liquefaction. In this study, two hyperthermophilic α-amylases with significant differences in thermostability, PfAmy and TeAmy, were comparatively studied through structural analysis, domain swapping, and site-directed mutagenesis, finding that three residues, His152, Cys166, and His168, located in domain B were the main contributors to hyperthermostability. The effects of these three residues were strongly synergistic, causing the optimum temperature for the mutant K152H/A166C/E168H of TeAmy to shift to 95-100 °C and stabilize at 90 °C without Ca²⁺. Compared to PfAmy and TeAmy, the mutant K152H/A166C/E168H, respectively, exhibited 1.7- and 2.5-times higher starch hydrolysis activity at 105 °C and pH 5.5 (10411 ± 70 U/mg) and released 1.1- and 1.7-times more maltooligosaccharides from 1% starch. This work has interpreted the hyperthermophilic mechanism of α-amylase and thereby providing a potential candidate for the efficient industrial conversion of starch to bioproducts.

Molecular Dynamics Simulations Reveal the Conformational Transition of GH33 Sialidases

Sialidases are increasingly used in the production of sialyloligosaccharides, a significant component of human milk oligosaccharides. Elucidating the catalytic mechanism of sialidases is critical for the rational design of better biocatalysts, thereby facilitating the industrial production of sialyloligosaccharides. Through comparative all-atom molecular dynamics simulations, we investigated the structural dynamics of sialidases in Glycoside Hydrolase family 33 (GH33). Interestingly, several sialidases displayed significant conformational transition and formed a new cleft in the simulations. The new cleft was adjacent to the innate active site of the enzyme, which serves to accommodate the glycosyl acceptor. Furthermore, the residues involved in the specific interactions with the substrate were evolutionarily conserved in the whole GH33 family, highlighting their key roles in the catalysis of GH33 sialidases. Our results enriched the catalytic mechanism of GH33 sialidases, with potential implications in the rational design of sialidases.

Rational design of enzyme activity and enantioselectivity

The strategy of rational design to engineer enzymes is to predict the potential mutants based on the understanding of the relationships between protein structure and function, and subsequently introduce the mutations using the site-directed mutagenesis. Rational design methods are universal, relatively fast and have the potential to be developed into algorithms that can quantitatively predict the performance of the designed sequences. Compared to the protein stability, it was more challenging to design an enzyme with improved activity or selectivity, due to the complexity of enzyme molecular structure and inadequate understanding of the relationships between enzyme structures and functions. However, with the development of computational force, advanced algorithm and a deeper understanding of enzyme catalytic mechanisms, rational design could significantly simplify the process of engineering enzyme functions and the number of studies applying rational design strategy has been increasing. Here, we reviewed the recent advances of applying the rational design strategy to engineer enzyme functions including activity and enantioselectivity. Five strategies including multiple sequence alignment, strategy based on steric hindrance, strategy based on remodeling interaction network, strategy based on dynamics modification and computational protein design are discussed and the successful cases using these strategies are introduced.