Thermostability engineering of industrial enzymes through structure modification

Rational design strategy for thermostability enhancement of protein-glutaminase and investigation of the underlying mechanisms

Protein-Glutaminase (PG) with efficient deamidation ability has shown vital potential in food fields. Enzymes with high thermostability remain active in high-temperature environments, which can be applied to some steps requiring high temperature treatment in food processing, thereby greatly expanding their industrial application. In this study, an efficient comprehensive strategy based on consensus sequence and computer-aid analysis was proposed to develop a combinatorial mutant mPG-5M (A79S/T97V/S108P/N154D/L156Y), exhibiting a 55.1-fold increase in t1/2 at 60 °C (1132.75 min) and a Tm value of 75.21 °C without loss of enzyme activity. Molecular dynamics simulation analysis insisted that the reduced flexibility, increased structural rigidity, and enhanced hydrogen bonding network observed in the mPG-5M all contribute to its superior stability, particularly under thermal stress. This study provided valuable strategy and comprehensive molecular mechanisms insights for protein engineering of the thermostability enhancement of PG, broadening its industrial applicability of food protein deamidation. These mutations collectively contributed to the enhanced thermal stability of the mPG-5M mutant.

Covalently immobilized β-galactosidase onto a novel alginate/lemon peel carrier: Catalytic, kinetic, stability studies, and its application in the production of whey high-protein beverage

β-Galactosidase (βG) was immobilized on novel alginate/lemon peel (Alg/LP) beads, achieving an immobilization yield of 84.7 % and an efficiency of 96.6 %. Both free and immobilized enzymes exhibited optimal activity at 50 °C and pH 5. The immobilized enzyme (Alg/LP/βG) demonstrated significantly improved thermal stability and broader pH tolerance compared to its free form. Immobilization notably altered enzyme kinetics, reducing Km by 57 % and Vmax by 13.4 %. Alg/LP/βG displayed excellent storage stability at 4 °C, retaining 91.3 % activity after 21 days and 79.6 % activity after 35 days. It also maintained 100 % activity after 11 cycles and 75.4 % activity after 15 operational cycles. The enzyme's application was explored in producing high-protein beverages from 13 % whey protein concentrate, enhancing sweetness by hydrolyzing lactose into glucose and galactose, which were further sweetened with 7 % sucrose. Adding lemon peel powder (LPP) improved the beverage's flavor, antioxidant properties, total phenolic content, and viscosity while keeping its chemical composition low. Sensory evaluation identified the beverage with 0.4 % LPP as the most preferred. This study highlights the potential of Alg/LP beads as an effective support matrix for β-galactosidase, offering enhanced stability, reusability, and applicability, particularly for enzymatic processes in the food industry.

Molecular modification and preliminary application of a novel mannanase from Alkalihalobacillus hemicellulosilyticus

Mannooligosaccharides (MOS) are high-quality prebiotic components, and enzymatic production of MOS is the most efficient, simple, and environmentally friendly method. Mannanase is the key enzyme involved in the decomposition of mannan for MOS production. However, there are currently challenges in obtaining thermally stable Mannanase. In this study, a novel thermo-alkaline mannanase, ManB085, was discovered from Alkalihalobacillus hemicellulosilyticus and heterologously expressed. The optimal temperature and pH of this enzyme are 75 °C and 10, respectively, and it remains stable at pH 7-12 and temperatures below 50 °C. Through rational design, a mutant ManB085M, with the non-catalytic domain truncated, was obtained, showing significantly improved thermal stability. The half-life of the mutant at 75 °C is 12.3 times that of the wild type, and the T50 increased by 23 °C. Notably, the enzyme can also produce MOS by hydrolyzing hemicellulose in coffee grounds. To enhance the MOS production capability, a Carbohydrate-Binding Module (CBM) was added to the C-terminus of ManB085M, significantly improving its ability to extract MOS from coffee grounds. This study proposes a novel mannanase with significant potential in MOS production.

Recent Advancements for Enhanced Biocatalyst and Biotransformation

Enzymes are essential biological macromolecules with various biological and industrial applications. As modern applications of enzymes as biocatalysts are increasingly explored, the demand for enzymes with improved catalytic properties is also increasing exponentially. Since most commercially available enzymes have a problem with long-term stability and activity under various industrial conditions, the exploration of different environments using omics technology and biotransformation of these proteins to improve stability is being recognized. Direct evolution, structure-based rational design, or de novo synthesis methods are used for enzyme engineering and developing novel enzymes with unique catalytic activity and high stability. The review provides an overview of the different classes of industrially important enzymes, their sources, and the various enzyme engineering methods used to increase their efficiency. The importance of enzyme engineering concerning the development of other techniques in the field of molecular biology is also examined.

Modifying loop regions in lipase from Caldibacillus thermoamylovorans for enhancing thermostability

Lipases are widely used as green industrial catalysts. Lipases from thermophilic microorganisms are particularly valuable due to their expected thermostability. However, the natural catalytic abilities and tolerance to extreme conditions of most enzymes are often not directly suited to the demands of industrial applications. Enzyme thermostability is closely associated with its structure, making it a target for improving enzyme thermostability. Therefore, we obtained the crystal structure of lipase from Caldibacillus thermoamylovorans (CtLip) with a resolution of 2.2 Å using X-ray diffraction and identified its optimal temperature at 50 °C, with a half-life (t1/2) of 21.59 min at 50 °C. Mutants B1 (R269E/G270S/V271I/V272L), A335I and the stacked mutant B1/A335I (R269E/G270S/V271I/V272L/A335I) in loop region were constructed under the guidance of molecular dynamics analysis. Optimal temperature of mutant B1/A335I increased by 5 °C, with a half-life 8.36 times longer than that of the wild-typed. Our findings provide strategies to improve lipase thermostability by modification of the loop region of the enzyme.

Directed Evolution of an (R)-Selective Transaminase Toward Higher Efficiency of Sitagliptin Analog Biosynthesis

Transaminase (TA)-catalyzed asymmetric amination is considered as a green chemistry approach to synthesize pharmaceutical analogs, but their ability to accept substrate for catalyzing sterically hindered ketones remains a challenge. Sitagliptin is an antihyperglycemic drug to treat type II diabetes. Herein, we exploited an efficient (R)-selective TA to biosynthesize sitagliptin analog (R)-3-amino-1-morpholino-4-(2,4,5-trifluorophenyl)butan-1-one. Starting from a previously constructed (R)-ATA5, two rounds of directed evolution were performed through combining error-prone PCR, site-directed saturation and combinatorial mutagenesis. The resultant variant ATA5/F189H/S236T/M121H showed a 10.2-fold higher activity and a 4-fold improved half-life at 45°C. Crucially, the variant was able to either catalyze the amination of 700 mM substrate with a conversion up to 93.1% and product e.e.> 99% in a cosolvent reaction system, or biotransform 200 mM substrate with a conversion of 97.6% and product e.e.> 99% in a cosolvent-free system. Furthermore, the structural analysis gave insight into how the mutations affected enzymatic activity and thermostability. This study, which consists of constructing a robust (R)-selective TA and the new synthesis route with the highest conversion ever reported, provides a reference for industrial manufacturing sitagliptin analog.

Improving the thermostability and substrate affinity of IsPETase through the S209H mutation, and exploring the structural role of the N-terminal: a computational study

The current in silico investigation aimed to increase the thermostability of IsPETase for more efficient PET degradation. N-Truncated and S209H mutants were designed to improve the thermostability of IsPETase. The deletion of the first seven N-terminal residues in PETase (N-truncated mutant) disrupts structural integrity, as Arg5, a crucial residue, maintains stability by forming a hydrogen bond network with Pro2, Thr48, Lys230, and Arg238. This links the N-terminal to the C-terminal, while its absence increases RMSF values in this region. The S209H mutation, located in the catalytic loop of IsPETase, enhances thermostability by introducing a new hydrophobic interaction with residue W130. MD simulations at 353.15 K have demonstrated this improvement, showing reduced structural flexibility and compactness in the S209H mutant compared to the WT. Specifically, the overall RMSD, Cα RMSD, SASA, and Rg values decreased from 3.36249 ± 0.853 Å, 1.321843 ± 0.0953 Å, 10,057.73 ± 135.11 Å2, and 17.09687 ± 1.387 Å in the WT to 3.184878 ± 0.786 Å, 0.969998 ± 0.119 Å, 9894.527 ± 118.53 Å2, and 16.962 ± 1.265 Å in the S209H mutant, respectively. Molecular docking revealed binding energies of -4.9 kcal/mol for WT, -5.1 kcal/mol for the S209H mutant, and -4.8 kcal/mol for the N-truncated mutant. MM-PBSA analysis using YASARA showed that the S209H mutation increased binding energy from -17.3606 kJ/mol (WT) to -7.82077 kJ/mol, enhancing binding affinity, while the N-truncated mutant reduced binding energy to -23.5032 kJ/mol, lowering binding affinity. In conclusion, this study has demonstrated that the S209H mutation enhanced the thermostability and the PET affinity of IsPETase by introducing the hydrophobic interactions. The N-truncated mutant reduced both thermostability and PET affinity, highlighting the critical role of the N-terminal region in maintaining the stability and activity of IsPETase.

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.

In Silico Structural Insights into a Glucanase from Clostridium perfringens and Prediction of Structural Stability Improvement Through Hydrophobic Interaction Network and Aromatic Interaction

Glucanases are widely applied in industrial applications such as brewing, biomass conversion, food, and animal feed. Glucanases catalyze the hydrolysis of glucan to produce the sugar hemiacetal through hydrolytic cleavage of glycosidic bonds. Current study aimed to investigate structural insights of a glucanase from Clostridium perfringens through blind molecular docking, site-specific molecular docking, molecular dynamics (MD) simulation, and binding energy calculation. Furthermore, we aimed to enhance structural stabilization through formation of hydrophobic interaction network. The molecular docking results illustrated that residues Glu222 and Asp187 may act as nucleophile acid/base catalyst. Moreover, the MM/PBSA results illustrated a high binding affinity of 108.71 ± 8.5 kJ/mol between glucanase and barely glucan during 100 ns simulation. The RMSF analysis illustrated a high flexible surface loop with the highest mobility at position D130. Therefore, the structural engineering was carried out through introducing a double-mutant S125Y/D130P, and the structural stability was improved by forming the hydrophobic interaction network and one π-π aromatic interaction. The spatial distance between the mutation sites and the catalytic pocket attenuates their direct impact on binding interactions within the catalytic pocket.

Recent advances in phytase thermostability engineering towards potential application in the food and feed sectors

This review comprehensively examines the advancements in engineering thermostable phytase through genetic modification and immobilization techniques, focusing on developments from the last seven years. Genetic modifications, especially protein engineering, have enhanced enzyme's thermostability and functionality. Immobilization on various supports has further increased thermostability, with 50-60 % activity retention at higher temperature (more than 50 °C). In the food industry, phytase is used in flour processing and bread making, reducing phytate content by around 70 %, thereby improving nutritional value and mineral bioavailability. In the feed industry, it serves as a poultry feed additive, breaking down phytates to enhance nutrient availability and feed efficiency. The enzyme's robustness at high temperatures makes it valuable in feed processing. The integration of microbial production of phytase with genetically engineered strains followed by carrier free immobilization represents a synergistic approach to fortify enzyme structure and improve thermal stability. These advancement in the development of phytase enzyme capable of withstanding high temperatures, thereby pivotal for industrial utilization.

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.

Reengineering the Substrate Tunnel to Enhance the Catalytic Efficiency of Squalene Epoxidase

Squalene epoxidase plays a pivotal role in the biosynthesis of ergosterol, its derivatives, and other triterpenoid compounds by catalyzing the transformation of squalene into 2,3-oxidosqualene. However, its low catalytic efficiency remains a primary bottleneck for the microbial synthesis of triterpenoids. In this study, the catalytic activity of the squalene epoxidase from Saccharomyces cerevisiae was significantly improved by reshaping its substrate tunnel, resulting in a marked increase in the yield of the final product, ergosterol. First, the amino acid in the catalytic pocket of squalene epoxidase was replaced with alanine (Ala), effectively reducing the steric hindrance, and thus, enhancing the affinity of the enzyme with its substrate. Then, the V249H/L343A mutant was obtained by redesigning the substrate tunnel of dominant mutant L343A, thus, increasing the titer of ergosterol. The study also elucidated the mechanism behind the increased catalytic activity of the V249H/L343A mutant through substrate tunnel parameter analysis and molecular dynamics simulations. Finally, a titer of 3345 mg/L of ergosterol was achieved by strains containing V249H/L343A in a 5 L bioreactor, with a specific yield of 84 mg/g dry cell weight (DCW), marking a 64% increase compared with the titer achieved by wild type strains. This study established a strong foundation for improving the synthetic efficiency of ergosterol and other triterpenoid compounds.

Mechanistic analysis of thermal stability in a novel thermophilic polygalacturonase MlPG28B derived from the marine fungus Mucor lusitanicus

In this study, heterologous MlPG28B expression was obtained by cloning the Mucor lusitanicus gene screened from a marine environment. The enzyme activity of MlPG28B was maximum at 60 °C, 30 % of the enzyme activity was retained after incubation at 100 °C for 30 min, and enzyme activity was still present after 60 min incubation, one of the best thermostable polygalacturonases characterized until now. The high-purity oligosaccharide standards (DP2-DP7) were prepared with polygalacturonic acid as a substrate. Kinetic parameters showed that MlPG28B at the optimum temperature has a low Km value (3055 ± 1104 mg/L), indicating high substrate affinity. Sequence alignment analysis inferred key residues Cys276, Cys284, Lys107, and Gln237 for MlPG28B thermal stability. Molecular docking and molecular dynamics simulation results indicated that MlPG28B has flexible T1 and T3 loops conducive to substrate recognition, binding, and catalysis and forms a hydrogen bond to the substrate by a highly conserved residue Asn161 in the active-site cleft. Based on site-directed mutation results, the five residues are key in determining MlPG28B thermal stability. Therefore, MlPG28B is a promising candidate for industrial enzymes in feed preparation.

Zearalenone degrading enzyme evolution to increase the hydrolysis efficiency under acidic conditions by the rational design

Based on rational design, zearalenone degrading enzyme was evolved to improve the hydrolysis efficiency under acidic conditions. At pH 4.2 and 37 °C, the activity of the zearalenone degrading enzyme evolved with 8 mutation sites increased from 7.69 U/mg to 38.67 U/mg. Km of the evolved zearalenone degrading enzyme decreased from 283.61 μM to 75.33 μM. The evolved zearalenone degrading enzyme was found to effectively degrade zearalenone in pig stomach chyme. Molecular docking revealed an increase in the number of hydrogen bonds and π-sigma interactions between the evolved zearalenone degrading enzyme and zearalenone. The evolved zearalenone degrading enzyme was valuable for hydrolyzing zearalenone under acidic conditions.

Continuous Flow Microreactors for the High-efficiency Enzymatic Synthesis of 10-Hydroxystearic Acid from Oleic Acid

Converting fatty acids into specialty chemicals is sustainable but hindered by the low efficiency and thermal instability of current oleic acid hydratases, along with mass transfer limitations in emulsion reactions. This study introduces an optimized continuous flow micro-reactor (CFMR) that efficiently transforms oleic acid at low (15 g L-1) and high (50 g L-1) concentrations, improving reaction efficiency and overcoming key conversion barriers. The first CFMR model showed reaction speeds surpassing traditional batch stirred tank reactors (BSTR). Optimizations were performed on three key components: liquid storage, mixer, and reaction section of the CFMR, with each round's best conditions carried into the next. This achieved a space-time yield of 597 g L-1 d-1 at a 15 g L-1 oleic acid load. To further enhance the yield, we optimized the emulsifier system to solve incomplete emulsification and developed a two-component feed microreactor (TCFMR) that addressed mass transfer limitations caused by the product at high substrate loads, reaching a 91 % conversion of 50 g L-1 oleic acid in 30 minutes, with a space-time yield of 2312 g L-1 d-1. These advancements represent significant progress in utilizing fatty acids and advancing sustainable chemical synthesis.

Enhancement of tryptophan 2-monooxygenase thermostability by semi-rational enzyme engineering: a strategic design to minimize experimental investigation

Tryptophan 2-monooxygenase (TMO) is an FAD-bound flavoenzyme which catalyzes the oxidative decarboxylation of l-tryptophan to produce indole-3-acetamide (IAM) and carbon dioxide. The reaction of TMO is the first step of indole-3-acetic acid (IAA) biosynthesis. Although TMO is of interest for mechanistic studies and synthetic biology applications, the enzyme has low thermostability and soluble expression yield. Herein, we employed a combined approach of rational design using computational tools with site-saturation mutagenesis to screen for TMO variants with significantly improved thermostability properties and soluble protein expression. The engineered TMO variants, TMO-PWS and TMO-PWSNR, possess melting temperatures (T m) of 65 °C, 17 °C higher than that of the wild-type enzyme (TMO-WT). At 50 °C, the stabilities (t 1/2) of TMO-PWS and TMO-PWSNR were 85-fold and 92.4-fold higher, while their soluble expression yields were 1.4-fold and 2.1-fold greater than TMO-WT, respectively. Remarkably, the kinetic parameters of these variants were similar to those of the wild-type enzymes, illustrating that they are promising candidates for future studies. Molecular dynamic simulations of the wild-type and thermostable TMO variants identified key interactions for enhancing these improvements in the biophysical properties of the TMO variants. The introduced mutations contributed to hydrogen bond formation and an increase in the regional hydrophobicity, thereby, strengthening the TMO structure.

Enhancing the Catalytic Activity of Geranylgeranyl Diphosphate Synthase through Ancestral Sequence Reconstruction and Semirational Design

Geranylgeranyl diphosphate synthase (GGPPS) is the crucial bottleneck in carotenoid biosynthesis. However, low activity limits the broad application of GGPPS. In this study, OsGGPPS1 in rice was engineered based on ancestral sequence reconstruction (ASR) and semirational design to improve the catalytic performances of existing GGPPS. The better mutant of A22R/A26P with improved enzyme activity was generated based on ASR. Additionally, the improved enzyme activity of mutants as V162A/M218S/F227Y was designed using a semirational design. The combinatorial assembly of the d-OsGGPPS1 mutant (A22R/A26P/V162A/M218S/F227Y) exhibited higher conversion of IPP and each cosubstrate of DMAPP for 9.8-fold in GPP production, GPP for 6.4-fold in FPP production, and FPP for 1.4-fold in GGPP production relative to wild-type OsGGPPS1 at 25 °C, which showed higher conversion than wild-type OsGGPPS1 at temperatures as high as 50 °C. The successful design of OsGGPPS1 was representative of protein engineering, which will shed new light on GGPPS engineering and active plant pigment resource utilization.

Integrated strategies for efficient production of Streptomyces mobaraensis transglutaminase in Komagataella phaffii

Transglutaminase (TGase) from Streptomyces mobaraensis commonly used to improve protein-based foods due to its unique enzymatic reactions, which imply considerable attention in its production. Recently, TGase exhibit broad market potential in non-food industries. However, achieving efficient synthesis of TGase remains a significant challenge. Herein, we achieved a substantial amount of a fully functional and kinetically stable TGase produced by Komagataella phaffii (Pichia pastoris) using multiple strategies including Geneticin (G418) screening, combinatorial mutations, promoter optimization, and co-expression. The active TGase expression reached a maximum of 10.1 U mL-1 in shake flask upon 96 h of induction, which was 3.8-fold of the wild type. Also, the engineered strain exhibited a 6.4-fold increase in half-life and a 2-fold increase in specific activity, reaching 172.67 min at 60 °C (t1/2(60 °C)) and 65.3 U mg-1, respectively. Moreover, the high-cell density cultivation in 5-L fermenter was also applied to test the productivity at large scale. Following optimization at a fermenter, the secretory yield of TGase reached 47.96 U mL-1 in the culture supernatant. Given the complexity inherent in protein expression and secretion, our research is of great significance and offers a comprehensive guide for improving the production of a wide range of heterologous proteins.

The two-step strategy for enhancing the specific activity and thermostability of alginate lyase AlyG2 with mechanism for improved thermostability

To overcome the trade-off challenge encountered in the engineering of alginate lyase AlyG2 from Seonamhaeicola algicola Gy8T and to expand its potential industrial applications, we devised a two-step strategy encompassing activity enhancement followed by thermal stability engineering. To enhance the specific activity of efficient AlyG2, we strategically substituted residues with bulky steric hindrance proximal to the active pocket with glycine or alanine. This led to the generation of three promising positive mutants, with particular emphasis on the T91S mutant, exhibiting a 1.91-fold specific activity compared to the wild type. To mitigate the poor thermal stability of T91S, mutants with negative ΔΔG values in the thermal flexibility region were screened out. Notably, the S72Ya mutant not only displayed 17.96 % further increase in specific activity but also exhibited improved stability compared to T91S, manifesting as a remarkable 30.97 % increase in relative activity following a 1-hour incubation at 42 °C. Furthermore, enhanced kinetic stability was observed. To gain deeper insights into the mechanism underlying the enhanced thermostability of the S72Ya mutant, we conducted molecular dynamics simulations, principal component analysis (PCA), dynamic cross-correlation map (DCCM), and free energy landscape (FEL) analysis. The results unveiled a reduction in the flexibility of the surface loop, a stronger correlation dynamic and a narrower motion subspace in S72Ya system, along with the formation of more stable hydrogen bonds. Collectively, our findings suggest amino acids substitutions resulting in smaller side chains proximate to the active site can positively impact enzyme activity, while reducing the flexibility of surface loops emerges as a pivotal factor in conferring thermal stability. These insights offer valuable guidance and a framework for the engineering of other enzyme types.

Characterization of a novel carboxylesterase from Streptomyces lividans TK24 and site-directed mutagenesis for its thermostability

As an industrial enzyme that catalyzes the formation and cleavage of ester bonds, carboxylesterase has attracted attention in fine chemistry, pharmaceutical, biological energy and bioremediation fields. However, the weak thermostability limits their further developments in industrial applications. In this work, a novel carboxylesterase (EstF) from Streptomyces lividans TK24, belonging to family XVII, was acquired by successfully heterologous expressed and biochemically identified. The EstF exhibited optimal activity at 55 °C, pH 9.0 and excellent catalytic performances (Km = 0.263 mM, kcat/Km = 562.3 s-1 mM-1 for p-nitrophenyl acetate (pNPA2) hydrolysis). Besides, the EstF presented exceptionally high thermostability with a half-life of 387.23 h at 55 °C and 2.86 h at 100 °C. Furthermore, the EstF was modified to obtain EstFP144G using the site-directed mutation technique to investigate the effect of single glycine on thermostability. Remarkably, the mutant EstFP144G displayed a 5.10-fold increase of half-life at 100 °C versus wild-type without affecting catalytic performance. Structural analysis implied that the glycine introduction could release a steric strain and induce cooperative effects between distal residues to increase the thermostability. Therefore, the thermostable EstF and EstFP144G with prominently catalytic characteristics have potential industrial applications and the introduction of a single glycine strategy opens up alternative avenues for the thermostability engineering of other enzymes.

Identification and characterization of a promiscuous metallohydrolase in metallo-β-lactamase superfamily from a locally isolated organophosphate-degrading Bacillus sp. strain S3wahi

In this present study, characteristics and structure-function relationship of an organophosphate-degrading enzyme from Bacillus sp. S3wahi were described. S3wahi metallohydrolase, designated as S3wahi-MH (probable metallohydrolase YqjP), featured the conserved αβ/βα metallo-β-lactamase-fold (MBL-fold) domain and a zinc bimetal at its catalytic site. The metal binding site of S3wahi-MH also preserves the H-X-H-X-D-H motif, consisting of specific amino acids at Zn1 (Asp69, His70, Asp182, and His230) and Zn2 (His65, His67, and His137). The multifunctionality of S3wahi-MH was demonstrated through a steady-state kinetic study, revealing its highest binding affinity (KM) and catalytic efficiency (kcat/KM) for OP compound, paraoxon, with values of 8.09 × 10-6 M and 4.94 × 105 M-1 s-1, respectively. Using OP compound, paraoxon, as S3wahi-MH native substrate, S3wahi-MH exhibited remarkable stability over a broad temperature range, 20 °C - 60 °C and a broad pH tolerance, pH 6-10. Corresponded to S3wahi-MH thermal stability characterization, the estimated melting temperature (Tm) was found to be 72.12 °C. S3wahi-MH was also characterized with optimum catalytic activity at 30 °C and pH 8. Additionally, the activity of purified S3wahi-MH was greatly enhanced in the presence of 1 mM and 5 mM of manganese (Mn2+), showing relative activities of 1323.68 % and 2073.68 %, respectively. The activity of S3wahi-MH was also enhanced in the presence of DMSO and DMF, showing relative activities of 270.37 % and 307.41 %, respectively. The purified S3wahi-MH retained >60 % residual activity after exposure to non-ionic Tween series surfactants. Nevertheless, the catalytic activity of S3wahi-MH was severely impacted by the treatment of SDS, even at low concentrations. Considering its enzymatic properties and promiscuity, S3wahi-MH emerges as a promising candidate as a bioremediation tool in wide industrial applications, including agriculture industry.

Coupling protein scaffold and biosilicification: A sustainable and recyclable approach for d-mannitol production via one-step purification and immobilization of multienzymes

Enzymatic synthesis of biochemicals in vitro is vital in synthetic biology for its efficiency, minimal by-products, and easy product separation. However, challenges like enzyme preparation, stability, and reusability persist. Here, we introduced a protein scaffold and biosilicification coupled system, providing a singular process for the purification and immobilization of multiple enzymes. Using d-mannitol as a model, we initially constructed a self-assembling EE/KK protein scaffold for the co-immobilization of glucose dehydrogenase and mannitol dehydrogenase. Under an enzyme-to-scaffold ratio of 1:8, a d-mannitol yield of 0.692 mol/mol was achieved within 4 h, 2.16-fold higher than the free enzymes. The immobilized enzymes retained 70.9 % of the initial joint activity while the free ones diminished nearly to inactivity after 8 h. Furthermore, we incorporated the biosilicification peptide CotB into the EE/KK scaffold, inducing silica deposition, which enabled the one-step purification and immobilization process assisted by Spy/Snoop protein-peptide pairs. The coupled system demonstrated a comparable d-mannitol yield to that of EE/KK scaffold and 1.34-fold higher remaining activities after 36 h. Following 6 cycles of reaction, the immobilized system retained the capability to synthesize 56.4 % of the initial d-mannitol titer. The self-assembly co-immobilization platform offers an effective approach for enzymatic synthesis of d-mannitol and other biochemicals.

Enhancing the stability of a novel D-allulose 3-epimerase from Ruminococcus sp. CAG55 by interface interaction engineering and terminally attached a self-assembling peptide

D-allulose, a highly desirable sugar substitute, is primarily produced using the D-allulose 3-epimerase (DAE). However, the availability of usable DAE enzymes is limited. In this study, we discovered and engineered a novel DAE Rum55, derived from a human gut bacterium Ruminococcus sp. CAG55. The activity of Rum55 was strictly dependent on the presence of Co2+, and it exhibited an equilibrium conversion rate of 30.6 % and a half-life of 4.5 h at 50 °C. To enhance its performance, we engineered the interface interaction of Rum55 to stabilize its tetramer structure, and the best variant E268R was then attached with a self-assembling peptide to form active enzyme aggregates as carrier-free immobilization. The half-life of the best variant E268R-EKL16 at 50 °C was dramatically increased 30-fold to 135.3 h, and it maintained 90 % of its activity after 13 consecutive reaction cycles. Additionally, we identified that metal ions played a key role in stabilizing the tetramer structure of Rum55, and the dependence on metal ions for E268R-EKL16 was significantly reduced. This study provides a useful route for improving the thermostability of DAEs, opening up new possibilities for the industrial production of D-allulose.

Computer-Aided Semi-Rational Design to Enhance the Activity of l-Sorbosone Dehydrogenase from Gluconobacter oxidans WSH-004

The titer of the microbial fermentation products can be increased by enzyme engineering. l-Sorbosone dehydrogenase (SNDH) is a key enzyme in the production of 2-keto-l-gulonic acid (2-KLG), which is the precursor of vitamin C. Enhancing the activity of SNDH may have a positive impact on 2-KLG production. In this study, a computer-aided semirational design of SNDH was conducted. Based on the analysis of SNDH's substrate pocket and multiple sequence alignment, three modification strategies were established: (1) expanding the entrance of SNDH's substrate pocket, (2) engineering the residues within the substrate pocket, and (3) enhancing the electron transfer of SNDH. Finally, mutants S453A, L460V, and E471D were obtained, whose specific activity was increased by 20, 100, and 10%, respectively. In addition, the ability of Gluconobacter oxidans WSH-004 to synthesize 2-KLG was improved by eliminating H2O2. This study provides mutant enzymes and metabolic engineering strategies for the microbial-fermentation-based production of 2-KLG.

Synthetic co-culture in an interconnected two-compartment bioreactor system: violacein production with recombinant E. coli strains

The concept of modular synthetic co-cultures holds considerable potential for biomanufacturing, primarily to reduce the metabolic burden of individual strains by sharing tasks among consortium members. However, current consortia often show unilateral relationships solely, without stabilizing feedback control mechanisms, and are grown in a shared cultivation setting. Such 'one pot' approaches hardly install optimum growth and production conditions for the individual partners. Hence, novel mutualistic, self-coordinating consortia are needed that are cultured under optimal growth and production conditions for each member. The heterologous production of the antibiotic violacein (VIO) in the mutually interacting E. coli-E. coli consortium serves as an example of this new principle. Interdependencies for growth control were implemented via auxotrophies for L-tryptophan and anthranilate (ANT) that were satisfied by the respective partner. Furthermore, VIO production was installed in the ANT auxotrophic strain. VIO production, however, requires low temperatures of 20-30 °C which conflicts with the optimum growth temperature of E. coli at 37 °C. Consequently, a two-compartment, two-temperature level setup was used, retaining the mutual interaction of the cells via the filter membrane-based exchange of medium. This configuration also provided the flexibility to perform individualized batch and fed-batch strategies for each co-culture member. We achieved maximum biomass-specific productivities of around 6 mg (g h)-1 at 25 °C which holds great promise for future applications.

Diverse models of cavity engineering in enzyme modification: Creation, filling, and reshaping

Most enzyme modification strategies focus on designing the active sites or their surrounding structures. Interestingly, a large portion of the enzymes (60%) feature active sites located within spacious cavities. Despite recent discoveries, cavity-mediated enzyme engineering remains crucial for enhancing enzyme properties and unraveling folding-unfolding mechanisms. Cavity engineering influences enzyme stability, catalytic activity, specificity, substrate recognition, and docking. This article provides a comprehensive review of various cavity engineering models for enzyme modification, including cavity creation, filling, and reshaping. Additionally, it also discusses feasible tools for geometric analysis, functional assessment, and modification of cavities, and explores potential future research directions in this field. Furthermore, a promising universal modification strategy for cavity engineering that leverages state-of-the-art technologies and methodologies to tailor cavities according to the specific requirements of industrial production conditions is proposed.

Automated in vivo enzyme engineering accelerates biocatalyst optimization

Achieving cost-competitive bio-based processes requires development of stable and selective biocatalysts. Their realization through in vitro enzyme characterization and engineering is mostly low throughput and labor-intensive. Therefore, strategies for increasing throughput while diminishing manual labor are gaining momentum, such as in vivo screening and evolution campaigns. Computational tools like machine learning further support enzyme engineering efforts by widening the explorable design space. Here, we propose an integrated solution to enzyme engineering challenges whereby ML-guided, automated workflows (including library generation, implementation of hypermutation systems, adapted laboratory evolution, and in vivo growth-coupled selection) could be realized to accelerate pipelines towards superior biocatalysts.

Application of an alchemical free energy method for the prediction of thermostable DuraPETase variants

Non-equilibrium (NEQ) alchemical free energy calculations are an emerging tool for accurately predicting changes in protein folding free energy resulting from amino acid mutations. In this study, this method in combination with the Rosetta ddg monomer tool was applied to predict more thermostable variants of the polyethylene terephthalate (PET) degrading enzyme DuraPETase. The Rosetta ddg monomer tool efficiently enriched promising mutations prior to more accurate prediction by NEQ alchemical free energy calculations. The relative change in folding free energy of 96 single amino acid mutations was calculated by NEQ alchemical free energy calculation. Experimental validation of ten of the highest scoring variants identified two mutations (DuraPETaseS61M and DuraPETaseS223Y) that increased the melting temperature (Tm) of the enzyme by up to 1 °C. The calculated relative change in folding free energy showed an excellent correlation with experimentally determined Tm resulting in a Pearson's correlation coefficient of r =  - 0.84. Limitations in the prediction of strongly stabilizing mutations were, however, encountered and are discussed. Despite these challenges, this study demonstrates the practical applicability of NEQ alchemical free energy calculations in prospective enzyme engineering projects. KEY POINTS: • Rosetta ddg monomer enriches stabilizing mutations in a library of DuraPETase variants • NEQ free energy calculations accurately predict changes in Tm of DuraPETase • The DuraPETase variants S223Y, S42M, and S61M have increased Tm.

A novel thermotolerant L-rhamnose isomerase variant for biocatalytic conversion of D-allulose to D-allose

A novel L-rhamnose isomerase was identified and cloned from an extreme-temperature aquatic habitat metagenome. The deduced amino acid sequence homology suggested the possible source of this metagenomic sequence to be Chloroflexus islandicus. The gene expression was performed in a heterologous host, Escherichia coli, and the recombinant protein L-rhamnose isomerase (L-RIM) was extracted and purified. The catalytic function of L-RIM was characterized for D-allulose to D-allose bioconversion. D-Allose is a sweet, rare sugar molecule with anti-tumour, anti-hypertensive, cryoprotective, and antioxidative properties. The characterization experiments showed L-RIM to be a Co++- or Mn++-dependent metalloenzyme. L-RIM was remarkably active (~ 80%) in a broad spectrum of pH (6.0 to 9.0) and temperature (70 to 80 °C) ranges. Optimal L-RIM activity with D-allulose as the substrate occurred at pH 7.0 and 75 °C. The enzyme was found to be excessively heat stable, displaying a half-life of about 12 days and 5 days at 65 °C and 70 °C, respectively. L-RIM catalysis conducted at slightly acidic pH of 6.0 and 70 °C achieved biosynthesis of about 30 g L-1 from 100 g L-1 D-allulose in 3 h. KEY POINTS: • The present study explored an extreme temperature metagenome to identify a novel gene that encodes a thermostable l-rhamnose isomerase (L-RIM) • L-RIM exhibits substantial (80% or more) activity in a broad spectrum of pH (6.0 to 9.0) and temperature (70 to 80 °C) ranges • L-RIM is excessively heat stable, displaying a half-life of about 12 days and 5 days at 65 °C and 70 °C, respectively.

Characterization of a novel 3-quinuclidinone reductase possessing remarkable thermostability

The 3-quinuclidinone reductase plays an irreplaceable role in the biopreparation of (R)-3-quinuclidinol, an intermediate vital for synthesis of various pharmaceuticals. Thermal robustness is a critical factor for enzymatic synthesis in industrial applications. This study characterized a new 3-quinuclidinone reductase, named SaQR, with significant thermal stability. The SaQR was overexpressed in a GST-fused state, and substrate and cofactor screening were conducted. Additionally, three-dimensional structure prediction using AlphaFold and analysis were performed, along with relevant thermostability tests, and the evaluation of factors influencing enzyme activity. The findings highlight the remarkable thermostability of SaQR, retaining over 90% of its activity after 72 h at 50°C, with an optimal operational temperature of 85°C. SaQR showed typical structural traits of the SDR superfamily, with its cofactor-determining residue being aspartic acid, conferring nicotinamide adenine dinucleotide (NAD(H)) preference. Moreover, K+ and Na+, at a concentration of 400 mM, could significantly enhance the activity, while Mg2+ and Mn2+ only display inhibitory effects within the tested concentration range. The findings of molecular dynamics simulations suggest that high temperatures may disrupt the binding of enzyme to substrate by increasing the flexibility of residues 205-215. In conclusion, this study reports a novel 3-quinuclidinone reductase with remarkable thermostability.

A Bibliometric Analysis: Current Perspectives and Potential Trends of Enzyme Thermostability from 1991-2022

Thermostability is considered a crucial parameter to evaluate the viability of enzymes in industrial applications. Over the past 31 years, many studies have been reported on the thermostability of enzymes. However, there is no systematic bibliometric analysis of publications on the thermostability of enzymes. In this study, 16,035 publications related to the thermostability of enzymes were searched and collected, showing an increasing annual trend. China contributed the most publications, while the United States had the highest citation count. International Journal of Biological Macromolecules is the most productive journal in the research field. Moreover, Chinese acad sci and Khosro Khajeh are the most active institutions and prolific authors in the field, respectively. Analysis of references with the strongest citation bursts and keyword co-occurrences, magnetic nanoparticles, metal-organic frameworks, molecular dynamics, and rational design are current hot spots and significant future research directions. This study is the first comprehensive bibliometric analysis summarizing trends and developments in enzyme thermostability research. Our findings could provide scholars with an understanding of the fundamental knowledge framework of the field and identify recent potential hotspots and research trends that could facilitate the discovery of collaboration opportunities.

Shifting the pH profiles of Staphylococcus epidermidis lipase (SEL) and Staphylococcus hyicus lipase (SHL) through generating chimeric lipases by DNA shuffling strategy

Enzymes are often required to function in a particular reaction condition by the industrial procedure. In order to identify critical residues affecting the optimum pH of Staphylococcal lipases, chimeric lipases from homologous lipases were generated via a DNA shuffling strategy. Chimeric 1 included mutations of G166S, K212E, T243A, H271Y. Chimeric 2 consisted of substitutions of K212E, T243A, H271Y. Chimeric 3 contained substitutions of K212E, R359L. From the screening results, the pH profiles for chimeric 1 and 2 lipases were shifted from pH 7 to 6. While the pH of chimeric 3 was shifted to 8. It seems the mutation of K212E in chimeric 1 and 2 decreased the pH to 6 by changing the electrostatic potential surface. Furthermore, chimeric 3 showed 10 ˚C improvement in the optimum temperature due to the rigidification of the catalytic loop through the hydrophobic interaction network. Moreover, the substrate specificity of chimeric 1 and 2 was increased towards the longer carbon length chains due to the mutation of T243A adjacent to the lid region through increasing the flexibility of the lid. Current study illustrated that directed evolution successfully modified lipase properties including optimum pH, temperature and substrate specificity through mutations, especially near catalytic and lid regions.

Insight on recently discovered PET polyester-degrading enzymes, thermostability and activity analyses

The flexibility and the low production costs offered by plastics have made them crucial to society. Unfortunately, due to their resistance to biological degradation, plastics remain in the environment for an extended period of time, posing a growing risk to life on earth. Synthetic treatments of plastic waste damage the environment and may cause damage to human health. Bacterial and fungal isolates have been reported to degrade plastic polymers in a logistic safe approach with the help of their microbial cell enzymes. Recently, the bacterial strain Ideonella sakaiensis (201-F6) was discovered to break down and assimilate polyethylene terephthalate (PET) plastic via metabolic processes at 30 °C to 37 °C. PETase and MHETase enzymes help the bacterium to accomplish such tremendous action at lower temperatures than previously discovered enzymes. In addition to functioning at low temperatures, the noble bacterium's enzymes have amazing qualities over pH and PET plastic degradation, including a shorter period of degradation. It has been proven that using the enzyme PETase, this bacterium hydrolyzes the ester linkages of PET plastic, resulting in production of terephthalic acid (TPA), nontoxic compound and mono-2-hydroxyethyl (MHET), along with further depolymerization of MHET to release ethylene glycogen (EG) and terephthalic acid (TPA) by the second enzyme MHETase. Enzymatic plastic degradation has been proposed as an environmentally friendly and long-term solution to plastic waste in the environment. As a result, this review focuses on the enzymes involved in hydrolyzing PET plastic polymers, as well as some of the other microorganisms involved in plastic degradation.

Improvement of the fibrinolytic activity, acid resistance and thermostability of nattokinase by surface charge engineering

Nattokinase is a promising thrombolytic drug due to its powerful fibrinolytic effect and few side effects. However, the low fibrinolytic activity and stability of nattokinase have limited its industrial production and oral application. In this study, the basic and neutral amino acid residues on the surface of recombinant nattokinase AprY from Bacillus mojavensis LY-06 (rAprY) were mutated to acidic amino acid residues by surface charge engineering strategy, and two variants K12D and N109D with 92.6 % and 8.4 % increased fibrinolytic activity were obtained. The R45E variant with enhanced acid stability and thermostability was also screened, its acid stability at pH 4 and t1/2 at 55 °C were 3.7-fold and 1.8-fold higher than that of wild type rAprY, respectively. Bioinformatics analysis showed that the increased activities of K12D and N109D variants were related to the increased flexibility of the region around their active centers. The increased rigidity of 97-103 amino acid residues around the active center of R45E may be the reason for its enhanced stability and reduced catalytic activity. The multipoint mutation K12D-N109D (M2)'s catalytic activity did not increase cumulatively, but its pH stability did. The nattokinase variants generated in this study have potential for industrial production and application.

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.

DeepTM: A deep learning algorithm for prediction of melting temperature of thermophilic proteins directly from sequences

Thermally stable proteins find extensive applications in industrial production, pharmaceutical development, and serve as a highly evolved starting point in protein engineering. The thermal stability of proteins is commonly characterized by their melting temperature (Tm). However, due to the limited availability of experimentally determined Tm data and the insufficient accuracy of existing computational methods in predicting Tm, there is an urgent need for a computational approach to accurately forecast the Tm values of thermophilic proteins. Here, we present a deep learning-based model, called DeepTM, which exclusively utilizes protein sequences as input and accurately predicts the Tm values of target thermophilic proteins on a dataset consisting of 7790 thermophilic protein entries. On a test set of 1550 samples, DeepTM demonstrates excellent performance with a coefficient of determination (R2) of 0.75, Pearson correlation coefficient (P) of 0.87, and root mean square error (RMSE) of 6.24 ℃. We further analyzed the sequence features that determine the thermal stability of thermophilic proteins and found that dipeptide frequency, optimal growth temperature (OGT) of the host organisms, and the evolutionary information of the protein significantly affect its melting temperature. We compared the performance of DeepTM with recently reported methods, ProTstab2 and DeepSTABp, in predicting the Tm values on two blind test datasets. One dataset comprised 22 PET plastic-degrading enzymes, while the other included 29 thermally stable proteins of broader classification. In the PET plastic-degrading enzyme dataset, DeepTM achieved RMSE of 8.25 ℃. Compared to ProTstab2 (20.05 ℃) and DeepSTABp (20.97 ℃), DeepTM demonstrated a reduction in RMSE of 58.85% and 60.66%, respectively. In the dataset of thermally stable proteins, DeepTM (RMSE=7.66 ℃) demonstrated a 51.73% reduction in RMSE compared to ProTstab2 (RMSE=15.87 ℃). DeepTM, with the sole requirement of protein sequence information, accurately predicts the melting temperature and achieves a fully end-to-end prediction process, thus providing enhanced convenience and expediency for further protein engineering.

Computational analysis of carboxylesterase genes and proteins in non-pathogenic food bacterium Alicyclobacillus acidocaldarius: insights from proteogenomics

Over recent years, Alicyclobacillus acidocaldarius, a Gram-positive nonpathogenic rod-shaped thermo-acid-tolerant bacterium, has posed numerous challenges for the fruit juice industry. However, the bacterium's unique characteristics, particularly its nonpathogenic and thermophilic capabilities, offer significant opportunities for genetic exploration by biotechnologists. This study presents the computational proteogenomics report on the carboxylesterase (CE) enzyme in A. acidocaldarius, shedding light on structural and evolutional of CEs from this bacterium. Our analysis revealed that the average molecular weight of CEs in A. acidocaldarius was 41 kDa, with an isoelectric point around 5. The amino acid composition favored negative amino acids over positive ones. The aliphatic index and hydropathicity were approximately 88 and - 0.15, respectively. While the protein sequence showed no disulfide bonds in the CEs' structure, the presence of Cys amino acids was observed in the structure of CEs. Phylogenetic analysis presented more than 99% similarity between CEs, indicating their close evolutionary relationship. By applying homology modeling, the 3-dimensional structural models of the carboxylesterase were constructed, which with the help of structural conservation and solvent accessibility analysis highlighted key residues and regions responsible for enzyme stability and conformation. The specific patterns presented the total solvent accessibility of less than 25 (Å2) was in considerable position as well as Gly residues were noticeably have high accessibility to solvent in all structures. Ala was the more frequent amino acids in the conserved-SASA of carboxylesterases. Furthermore, unsupervised agglomerative hierarchical clustering based on solvent accessibility feature successfully clustered and even distinguished this enzyme from proteases from the same genome. These findings contribute to a deeper understanding of the nonpathogenic A. acidocaldarius carboxylesterase and its potential applications in biotechnology. Additionally, structural analysis of CEs would help to address potential solutions in fruit juice industry with utilization of computational structural biology.

A thermostable organic solvent-tolerant lipase from Brevibacillus sp.: production and integrated downstream processing using an alcohol-salt-based aqueous two-phase system

Lipases are used for the synthesis of different compounds in the chemical, pharmaceutical, and food industries. Most of the reactions are carried out in non-aqueous media and often at elevated temperature, requiring the use of organic solvent-tolerant thermostable lipases. However, most known lipases are not stable in the presence of organic solvents and at elevated temperature. In this study, an organic solvent-tolerant thermostable lipase was obtained from Brevibacillus sp. SHI-160, a moderate thermophile isolated from a hot spring in the East African Rift Valley. The enzyme was optimally active at 65°C and retained over 90% of its activity after 1 h of incubation at 70°C. High lipase activity was measured in the pH range of 6.5 to 9.0 with an optimum pH of 8.5. The enzyme was stable in the presence of both polar and non-polar organic solvents. The stability of the enzyme in the presence of polar organic solvents allowed the development of an efficient downstream processing using an alcohol-salt-based aqueous two-phase system (ATPS). Thus, in the presence of 2% salt, over 98% of the enzyme partitioned to the alcohol phase. The ATPS-recovered enzyme was directly immobilized on a solid support through adsorption and successfully used to catalyze a transesterification reaction between paranitrophenyl palmitate and short-chain alcohols in non-aqueous media. This shows the potential of lipase SHI-160 to catalyze reactions in non-aqueous media for the synthesis of valuable compounds. The integrated approach developed for enzyme production and cheap and efficient downstream processing using ATPS could allow a significant reduction in enzyme production costs. The results also show the potential of extreme environments in the East African Rift Valley as sources of valuable microbial genetic resources for the isolation of novel lipases and other industrially important enzymes.

Improved secretory expression and characterization of thermostable xylanase and β-xylosidase from Pseudothermotoga thermarum and their application in synergistic degradation of lignocellulose

Xylanase and β-xylosidase are the key enzymes for hemicellulose hydrolysis. To further improve hydrolysis efficacy, high temperature hydrolysis with thermostable hemicellulases showed promise. In this study, thermostable xylanase (Xyn) and β-xylosidase (XynB) genes from Pseudothermotoga thermarum were cloned and secretory expressed in Bacillu subtilis. Compared with Escherichia coli expression host, B. subtilis resulted in a 1.5 time increase of enzymatic activity for both recombinant enzymes. The optimal temperature and pH were 95°C and 6.5 for Xyn, and 95°C and 6.0 for XynB. Thermostability of both recombinant enzymes was observed between the temperature range of 75-85°C. Molecular docking analysis through AutoDock showed the involvement of Glu525, Asn526, Trp774 and Arg784 in Xyn-ligand interaction, and Val237, Lys238, Val761 and Asn76 in XynB-ligand interaction, respectively. The recombinant Xyn and XynB exhibited synergistic hydrolysis of beechwood xylan and pretreated lignocellulose, where Xyn and XynB pre-hydrolysis achieved a better improvement of pretreated lignocellulose hydrolysis by commercial cellulase. The observed stability of the enzymes at high temperature and the synergistic effect on lignocellulosic substrates suggested possible application of these enzymes in the field of saccharification process.

Combined Computer-Aided Predictors to Improve the Thermostability of Nattokinase

Food-derived nattokinase has strong thrombolytic activity and few side effects. In the field of medicine, nattokinase has been developed as an adjuvant drug for the treatment of thrombosis, and nattokinase-rich beverages and health foods have also shown great potential in the field of food development. At present, the poor thermostability of nattokinase limits its industrial production and application. In this study, we used several thermostability-prediction algorithms to predict nattokinase from Bacillus mojavensis LY-06 (AprY), and screened two variants S33T and T174V with increased thermostability and fibrinolytic activity. The t1/2 of S33T and T174V were 8.87-fold and 2.51-fold those of the wild type AprY, respectively, and their enzyme activities were also increased (1.17-fold and 1.28-fold, respectively). Although the thermostability of N218L was increased by 2.7 times, the fibrinolytic activity of N218L was only 73.3% of that of wild type AprY. The multiple-point mutation results showed that S33T-N218L and S33T-T174V-N218L variants lost their activity, and the T174V-N218L variant did not show any significant change in catalytic performance, while S33T-T174V increased its thermostability and activity by 21.3% and 24.8%, respectively. Although the S33T-T174V variant did not show the additive effect of thermostability, it combined the excellent transient thermostability of S33T with the better thrombolytic activity of T174V. Bioinformatics analysis showed that the overall structure of S33T and T174V variants tended to be stable, while the structure of S33T-T174V variant was more flexible. Local structure analysis showed that the increased rigidity of the active center region (positions 64-75) and the key loop region (positions 129-130, 155-163, 187-192, 237-241, and 268-270) determined the increased thermostability of all variants. In addition, the enhanced flexibility of S33T-T174V variant in the Ca1 binding region (positions 1-4, 75-82) and the peripheral region of the catalytic pocket (positions 210-216) may account for the inability to superpose its thermostability. We explored the effective strategy to enhance the thermostability of nattokinase, and the resulting variants have potential industrial production and application.

Bioengineered Enzymes and Precision Fermentation in the Food Industry

Enzymes have been used in the food processing industry for many years. However, the use of native enzymes is not conducive to high activity, efficiency, range of substrates, and adaptability to harsh food processing conditions. The advent of enzyme engineering approaches such as rational design, directed evolution, and semi-rational design provided much-needed impetus for tailor-made enzymes with improved or novel catalytic properties. Production of designer enzymes became further refined with the emergence of synthetic biology and gene editing techniques and a plethora of other tools such as artificial intelligence, and computational and bioinformatics analyses which have paved the way for what is referred to as precision fermentation for the production of these designer enzymes more efficiently. With all the technologies available, the bottleneck is now in the scale-up production of these enzymes. There is generally a lack of accessibility thereof of large-scale capabilities and know-how. This review is aimed at highlighting these various enzyme-engineering strategies and the associated scale-up challenges, including safety concerns surrounding genetically modified microorganisms and the use of cell-free systems to circumvent this issue. The use of solid-state fermentation (SSF) is also addressed as a potentially low-cost production system, amenable to customization and employing inexpensive feedstocks as substrate.

Behavior of enzymes under high pressure in food processing: mechanisms, applications, and developments

High pressure processing (HPP) offers the benefits of safety, uniformity, energy-efficient, and low waste, which is widely applied for microbial inactivation and shelf-life extension for foods. Over the past forty years, HPP has been extensively researched in the food industry, enabling the inactivation or activation of different enzymes in future food by altering their molecular structure and active site conformation. Such activation or inactivation of enzymes effectively hinders the spoilage of food and the production of beneficial substances, which is crucial for improving food quality. This paper reviews the mechanism in which high pressure affects the stability and activity of enzymes, concludes the roles of key enzymes in the future food processed using high pressure technologies. Moreover, we discuss the application of modified enzymes based on high pressure, providing insights into the future direction of enzyme evolution under complex food processing conditions (e.g. high temperature, high pressure, high shear, and multiple elements). Finally, we conclude with prospects of high pressure technology and research directions in the future. Although HPP has shown positive effects in improving the future food quality, there is still a pressing need to develop new and effective combined processing methods, upgrade processing modes, and promote sustainable lifestyles.

Simultaneous enhancement of thermostability and catalytic activity of κ-carrageenase from Pseudoalteromonas tetraodonis by rational design

κ-Carrageenase provides an attractive enzymatic approach to preparation of κ-carrageenan oligosaccharides. Pseudoalteromonas tetraodonis κ-carrageenase is active at the alkaline conditions but displays low thermostability. To further improve its enzymatic performance, two mutants of Q42V and I51H exhibiting both improved thermostability and enzyme activity were screened by the PoPMuSiC algorithm. Compared with the wild-type κ-carrageenase (WT), Q42V and I51H increased the enzyme activity by 20.9% and 25.4%, respectively. After treatment at 50 ℃ for 40 min, Q42V and I51H enhanced the residual activity by 31.1% and 25.9%, respectively. The T_m values of Q42V, I51H, and WT determined by differential scanning calorimetry were 58.2 ℃, 54.8 ℃, and 51.2 ℃, respectively. Compared with untreated and HCl-treated κ-carrageenans, Q42V-treated κ-carrageenan exhibited higher pancreatic lipase inhibitory activity. Molecular docking analysis indicated that the additional pi-sigma force and hydrophobic interaction in the enzyme-substrate complex could account for the increased catalytic activity of Q42V and I51H, respectively. Molecular dynamics analysis indicated that the improved thermostability of mutants Q42V and I51H could be attributed to the less structural deviation and the flexible changes of enzyme conformation at high temperature. This study provides new insight into κ-carrageenase performance improvement and identifies good candidates for their industrial applications.

Automated optimisation of solubility and conformational stability of antibodies and proteins

Biologics, such as antibodies and enzymes, are crucial in research, biotechnology, diagnostics, and therapeutics. Often, biologics with suitable functionality are discovered, but their development is impeded by developability issues. Stability and solubility are key biophysical traits underpinning developability potential, as they determine aggregation, correlate with production yield and poly-specificity, and are essential to access parenteral and oral delivery. While advances for the optimisation of individual traits have been made, the co-optimization of multiple traits remains highly problematic and time-consuming, as mutations that improve one property often negatively impact others. In this work, we introduce a fully automated computational strategy for the simultaneous optimisation of conformational stability and solubility, which we experimentally validate on six antibodies, including two approved therapeutics. Our results on 42 designs demonstrate that the computational procedure is highly effective at improving developability potential, while not affecting antigen-binding. We make the method available as a webserver at www-cohsoftware.ch.cam.ac.uk.

Recent advances in simultaneous thermostability-activity improvement of industrial enzymes through structure modification

Engineered thermostable microbial enzymes are widely employed to catalyze chemical reactions in numerous industrial sectors. Although high thermostability is a prerequisite of industrial applications, enzyme activity is usually sacrificed during thermostability improvement. Therefore, it is vital to select the common and compatible strategies between thermostability and activity improvement to reduce mutants̕ libraries and screening time. Three functional protein engineering approaches, including directed evolution, rational design, and semi-rational design, are employed to manipulate protein structure on a genetic basis. From a structural standpoint, integrative strategies such as increasing substrate affinity; introducing electrostatic interaction; removing steric hindrance; increasing flexibility of the active site; N- and C-terminal engineering; and increasing intramolecular and intermolecular hydrophobic interactions are well-known to improve simultaneous activity and thermostability. The current review aims to analyze relevant strategies to improve thermostability and activity simultaneously to circumvent the thermostability and activity trade-off of industrial enzymes.

Immobilization and property of penicillin G acylase on amino functionalized magnetic Ni0.3Mg0.4Zn0.3Fe2O4 nanoparticles prepared via the rapid combustion process

Penicillin G acylase plays an important role in the biocatalytic process of semi-synthetic penicillin. In order to overcome the disadvantages of free enzymes and improve the catalytic performance of enzymes, it is a new method to immobilize enzymes on carrier materials. And magnetic materials have the characteristics of easy separation. In the present study, the Magnetic Ni0.3Mg0.4Zn0.3Fe2O4 nanoparticles were successfully prepared by a rapid-combustion method and calcined at 400°C for 2 h. The surface of the nanoparticles was modified with sodium silicate hydrate, and the PGA was covalently bound to the carrier particles through the cross-linking of glutaraldehyde. The results showed that the activity of immobilized PGA reached 7121.00 U/g. The optimum pH for immobilized PGA was 8 and the optimum temperature was 45°C, the immobilized PGA exhibited higher stability against changes in pH and temperature. The Michaelis–Menten constant (Km) values of the free and immobilized PGA were 0.00387 and 0.0101 mol/L and the maximum rate (Vmax) values were 0.387 and 0.129 μmol/min. Besides, the immobilized PGA revealed excellent cycling performance. The immobilization strategy presented PGA had the advantages of reuse, good stability, cost saving and had considerable practical significance for the commercial application of PGA.

Effects of synonymous mutations on kinetic properties and structure of firefly luciferase: Molecular dynamics simulation, molecular docking, RNA folding, and experimental study

Although synonymous mutations have long been thought to lack striking results, a growing body of research shows these mutations have highly variable effects. In this study, the impact of synonymous mutations in the development of thermostable luciferase was investigated using a combination of experimental and theoretical approaches. Using bioinformatics analysis, the codon usage features in the Lampyridae family's luciferases were studied and four synonymous mutations of Arg in luciferase were created. An exciting result was that the analysis of kinetic parameters showed a slight increase in the thermal stability of the mutant luciferase. AutoDock Vina, %MinMax algorithm, and UNAFold Server were used to perform molecular docking, folding rate, and RNA folding, respectively. Here, it was assumed that in the region (Arg337) with a moderate propensity for coil, synonymous mutation altered the rate of translation, which in turn may lead to a slight change in the structure of the enzyme. According to the molecular dynamics simulation data, local minor global flexibility is observed in the context of the protein conformation. A plausible explanation is that this flexibility may strengthen hydrophobic interactions due to its sensitivity to a molecular collision. Accordingly, thermostability originated mainly from hydrophobic interaction.

Role of distal sites in enzyme engineering

The limitations associated with natural enzyme catalysis have triggered the rise of the field of protein engineering. Traditional rational design was based on the analysis of protein structural information and catalytic mechanisms to identify key active sites or ligand binding sites to reshape the substrate pocket. The role and significance of functional sites in the active center have been studied extensively. With a deeper understanding of the structure-catalysis relationship map, the entire protein molecule can be filled with residues that play a substantial role in its structure and function. However, the catalytic mechanism underlying distal mutations remains unclear. The aim of this review was to highlight the criticality of the distal site in enzyme engineering based on the following three aspects: What can distal mutations exert on function from mutability landscape? How do distal sites influence enzyme function? How to predict and design distal mutations? This review provides insights into the catalytic mechanism of enzymes from the global interaction network, knowledge from sequence-structure-dynamics-function relationships, and strategies for distal mutation-based protein engineering.

Enhancing Acetophenone Tolerance of Anti-Prelog Short-Chain Dehydrogenase/Reductase EbSDR8 Using a Whole-Cell Catalyst by Directed Evolution

The short-chain dehydrogenase/reductase (SDR) from Empedobacter brevis ZJUY-1401 (EbSDR8, GenBank: ALZ42979.1) is a promising biocatalyst for the reduction of acetophenone to (R)-1-phenylethanol, but its industrial application is restricted by its insufficient tolerance to acetophenone. In this paper, we developed a chromogenic reaction-based high-throughput screening method and employed directed evolution to enhance the acetophenone tolerance of EbSDR8. The resulting variant, M190V, showed 74.8% improvement over the wild-type in specific activity when catalyzing the reduction of 200 mM acetophenone. Kinetic analysis revealed a 70% enhancement in its catalytic efficiency (kcat/Km). Molecular docking was conducted to reveal the possible mechanism behind the improved acetophenone tolerance, and the result implied that the M190V mutation is conducive to the binding and release of coenzyme. Aside from the improved catalytic performance when dealing with a high concentration of acetophenone, other features of M190V, such as a broad pH range (6.0 to 10.5), low optimal cosubstrate concentration (1% isopropanol), and a temperature optimum close to that of E. coli cells (35 °C), also contribute to its practical application as a whole-cell catalyst. In this study, we first designed a directed evolution means to engineer the enzyme and obtained the positive variant which has a high activity under high concentrations of acetophenone. After that, we optimized the catalytic performance of the variant to adapt to industrial applications.