Enhancing the thermostability of carboxypeptidase A by a multiple computer-aided rational design based on amino acids preferences at β-turns

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.

Overview of various protein engineering strategies to improve the catalytic activity, thermostability, and acid/base stability of β-glucanase

β-Glucan is highly valued in the food and medical industries due to its various physiological functions. However, its aqueous solution tends to have high viscosity, which negatively impacts the brewing and feed industries. By hydrolyzing β-glucosidic bonds, β-glucanase could reduce the adverse effects of β-glucan. For this reason, β-glucanase is widely utilized in the brewing and animal feed production. The limited thermal and acid stability of β-glucanase restricts its applications in industrial settings. Therefore, it is of great importance to enhance the stability of existing β-glucanases through protein engineering. This review summarizes current integrated technical methods for the molecular modification of β-glucanases, including error-prone PCR, site-saturation mutagenesis, DNA recombination, sequence alignment, N- and C-terminal modifications, surface charge optimization, intermolecular force optimization, and rigidity of flexible regions. The aim is to provide a theoretical basis and practical guidance for the further modification of β-glucanases.

Comprehensive Understanding of Laboratory Evolution for Food Enzymes: From Design to Screening Innovations

In the field of food processing, enzymes play a pivotal role in improving product quality and flavor, and extending shelf life. However, the exposure of traditional food enzymes to high temperatures during processing often leads to a decrease in activity or even inactivation, limiting the effectiveness of their application under high-temperature conditions. Therefore, the modification of thermostability and activity of enzymes to adapt to extreme conditions through protein engineering has become a key way to improve the efficiency and economic benefits of industrial production. Directed evolution and semirational design strategies in the laboratory have proven to be broadly applicable frameworks for biochemical researchers in the food field, including those who are beginners. In this review, we systematically summarize semirational design strategies and high-throughput screening strategies, and introduce some intuitive computer simulation software to improve the thermostability and enzyme activity of food enzymes. The application of these strategies and techniques provides a comprehensive guide for the optimization of food enzymes. In addition, the latest hot topics of genetically engineered food enzymes in the field of application are discussed.

Improvement the thermostability and specific activity of acidic xylanase PjxA from Penicillium janthinellum via rigid flexible sites

Acidic xylanase PjxA from Penicillium janthinellum MA21601, with good eosinophilic and enzymatic activity, is an excellent candidate for xylan degradation to achieve effective utilization of biomass materials. However, the low thermal stability of PjxA has become a major bottleneck in its application. In this study, the flexible sites of PjxA were identified and rigidified through computational simulations of structure and sequence analysis combined with folding free energy calculations. Finally, a combined mutase PjxA-DS was constructed by rational integration of the two single mutants S82N and D45N. Compared to PjxA, PjxA-DS showed a 115.11-fold longer half-life at 50 °C and a 2.02-fold higher specific enzyme activity. Computer simulation analysis showed that S82N and D45N acted synergistically to improve the thermostability of PjxA. The stabilization of the N-terminus and the active center of PjxA, the increase in surface positive charge and hydrophilicity are the main reasons for the improved thermostability and catalytic activity of PjxA. Rigidification of the flexible site is an effective method for improving the thermostability of enzymes, S82N and D45N can be used as effective targets for the thermostability engineering modification of GH11 acidic xylanase.

Surfactant-tolerance evolution of Bacillus clausii protease for enhancing activity and stability by reshaping the substrate access tunnel

Alkali proteases are crucial in numerous industries, especially in the laundry industry, but their inactivation by surfactants limits their effectiveness. This study employed substrate access tunnel engineering to improve the performance of WT bcPRO in surfactants. By modifying the key residues in the substrate pocket, the best variant N212S showed higher stability and activity in both AES and LAS. Molecular dynamics (MD) simulations provided insights into the enhanced stability and activity. The Asn212Ser mutation weakened the anti-correlation motion, increased the number of hydrogen bonds between amino acid residues, and made the protein structure more compact, contributing to its stability. Additionally, the mutation extended the substrate access tunnel and enabled additional interactions with the substrate, enhancing its catalytic activity in surfactants. This study demonstrates a strategy for reshaping the substrate access tunnel to improve protease stability and activity in surfactant environments, offering a promising protease candidate for the laundry industry.

Enhancement of thermostability and expression level of Rasamsonia emersonii lipase in Pichia pastoris and its application in biodiesel production in a continuous flow reactor

The acidic lipase from Rasamsonia emersonii named LIPR has great potential for biodiesel synthesis due to its strong methanol tolerance. Nonetheless, the limited thermostability of LIPR and low expression level in Escherichia coli remain major obstacles to its use in biodiesel synthesis. To enhance the thermostability, the mutant LIPR harboring mutations A126C-P238C for the formation of a new disulfide bond and amino acid substitution D214L was obtained through rational design. To our delight, the thermostability of LIPR mutant was greatly improved. Moreover, a comprehensive optimization strategy, such as employing the Mss signal peptide, co-expressing the molecular chaperone protein disulfide isomerase (PDI), knocking out the vacuolar sorting receptor gene VPS10-01, and overexpressing the dihydroxyacetone synthase gene DAS2, was adopted to obtain the combination-optimized mutant Pichia pastoris strain GS54. Furthermore, the biodiesel synthetic capability with the mutant GS54-LIPR was verified and the production yield was 52.2 % after 24 h in a shake flask. Subsequently, a continuous flow system was adopted to increase the biodiesel yield to 73.6 % within 3 h, demonstrating its efficacy in enhancing enzyme biocatalysis. The engineered GS54-LIPR mutant lipase is an efficient and reusable biocatalyst for the sustained production of biodiesel in a continuous flow reaction.

Characterization of thermostable carboxypeptidase from high-altitude hot spring metagenome

This study explored the metagenome of the Pir Panjal Hot Spring (PPHS) to identify thermostable hydrolases. The carboxypeptidase (CarP) gene was successfully amplified and cloned into Escherichia coli DH5-α cells, followed by expression in E. coli BL21-DE3 cells. The CarP enzyme was comprehensively characterized in vitro. Sequencing analysis revealed an open reading frame encoding a functional protein of 504 amino acids, with a molecular weight of 58.65 kDa and an isoelectric point of 4.81. The CarP protein was purified using Ni-His affinity chromatography, and the experimental molecular weight matched in silico predictions. The enzyme exhibited significant thermostability and alkaliphilic properties, with optimal activity at 70 °C and pH 10.0. Additionally, the presence of Zn+2 ions at concentrations of 5 and 10 mmol/L enhanced protease activity by 1.4 and 1.5-fold, respectively. This study reports the discovery of a novel, multifunctional, and thermostable CarP from hot-spring metagenomes. The enzyme's stability against high temperatures, metal ions, surfactants, and inhibitors, along with its specific substrate interactions, highlights its potential for various biotechnological applications.

Improving the substrate binding of acetyl-CoA carboxylase (AccB) from Streptomyces antibioticus through computational enzyme engineering

Malonyl-CoA serves as the main building block for the biosynthesis of many important polyketides, as well as fatty acid-derived compounds, such as biofuel. Escherichia coli, Corynebacterium gultamicum, and Saccharomyces cerevisiae have recently been engineered for the biosynthesis of such compounds. However, the developed processes and strains often have insufficient productivity. In the current study, we used enzyme-engineering approach to improve the binding of acetyl-CoA with ACC. We generated different mutations, and the impact was calculated, which reported that three mutations, that is, S343A, T347W, and S350W, significantly improve the substrate binding. Molecular docking investigation revealed an altered binding network compared to the wild type. In mutants, additional interactions stabilize the binding of the inner tail of acetyl-CoA. Using molecular simulation, the stability, compactness, hydrogen bonding, and protein motions were estimated, revealing different dynamic properties owned by the mutants only but not by the wild type. The findings were further validated by using the binding-free energy (BFE) method, which revealed these mutations as favorable substitutions. The total BFE was reported to be -52.66 ± 0.11 kcal/mol for the wild type, -55.87 ± 0.16 kcal/mol for the S343A mutant, -60.52 ± 0.25 kcal/mol for T347W mutant, and -59.64 ± 0.25 kcal/mol for the S350W mutant. This shows that the binding of the substrate is increased due to the induced mutations and strongly corroborates with the docking results. In sum, this study provides information regarding the essential hotspot residues for the substrate binding and can be used for application in industrial processes.

Removal of ochratoxin A in wine by Cryptococcus albidus and safety assessment of degradation products

BACKGROUND

Ochratoxin A (OTA) is a mycotoxin that contaminates grape-based products and is extremely harmful to the health of the host. It is effectively removed by yeast during the fermentation of wine, whereas the removal mechanism of OTA remains unclear. Therefore, the present study aimed to investigate the removal mechanism of ochratoxin A by yeast and to evaluate the safety of its degradation products.

RESULTS

Cryptococcus albidus (20-G) with better effect on ochratoxin A (OTA) was screened out in the main fermentation stage of wine. The results showed that 20-G removed OTA through biosorption and biodegradation. Intracellular enzymes played the main role (18.44%) and yeast cell walls adsorbed a small amount of OTA (8.44%). Furthermore, the identification of proteins in 20-G revealed that the decrease in OTA content was mainly a result of the action of peroxidase, and validation tests were carried out. By analyzing the degradation products of OTA, OTα and phenylalanine with lower toxicity were obtained. Animal experiments showed that the intervention of yeast 20-G reduced the damage and adverse effects caused by OTA toxicity to the mice.

CONCLUSION

The present study demonstrates the mechanism of OTA removal by 20-G and the toxicity of OTA was reduced by peroxidase in 20-G. © 2023 Society of Chemical Industry.