Enhanced Thermostability of D-Psicose 3-Epimerase from Clostridium bolteae through Rational Design and Engineering of New Disulfide Bridges

A disulfide bond mutant of Pseudoalteromonas porphyrae κ-carrageenase conferred improved thermostability and catalytic activity and facilitated its utilization in κ-carrageenan industrial waste residues recycling

In this study, Discovery Studio was employed to predict the potential disulfide bond mutants of the catalytic domain of Pseudoalteromonas porphyrae κ-carrageenase to improve the catalytic activity and thermal stability. The mutant N205C-G239C was identified with significantly increased catalytic activity toward κ-carrageenan substrate, with activity 4.28 times that of WT. The optimal temperature of N205C-G239C was 55 °C, 15 °C higher than that of WT. For N205C-G239C, the t1/2 value at 50 °C was 52 min, 1.41 times that of WT. The microstructural analysis revealed that the introduced disulfide bond N205C-G239C could create a unique catalytic environment by promoting favorable interactions with κ-neocarratetraose. This interaction impacted various aspects such as product release, water molecule network, thermodynamic equilibrium, and tunnel size. Molecular dynamics simulations demonstrated that the introduced disulfide bond enhanced the overall structure rigidity of N205C-G239C. The results of substrate tunnel analysis showed that the mutation led to the widening of the substrate tunnel. The above structure changes could be the possible reasons responsible for the simultaneous enhancement of the catalytic activity and thermal stability of mutant N205C-G239C. Finally, N205C-G239C exhibited the effective hydrolysis of the κ-carrageenan industrial waste residues, contributing to the recycling of the oligosaccharides and perlite.

Enhanced Thermostability of Nattokinase by Computation-Based Rational Redesign of Flexible Regions

Nattokinase is a nutrient in healthy food natto that has the function of preventing and treating blood thrombus. However, its low thermostability and fibrinolytic activity limit its application in food and pharmaceuticals. In this study, we used bioinformatics analysis to identify two loops (loop10 and loop12) in the flexible region of nattokinase rAprY. Using this basis, we screened the G131S-S161T variant, which showed a 2.38-fold increase in half-life at 55 °C, and the M3 variant, which showed a 2.01-fold increase in activity, by using a thermostability prediction algorithm. Bioinformatics analysis revealed that the enhanced thermostability of the G131S-S161T variant was due to the increased rigidity and structural shrinkage of the overall structure. Additionally, the increased rigidity of the local region surrounding the active center and its mutated sites helps maintain its normal conformation in high-temperature environments. The increased catalytic activity of the M3 variant may be due to its more efficient substrate binding mechanism. We investigated strategies to improve the thermostability and fibrinolytic activity of nattokinase, and the resulting variants show promise for industrial production and application.

Impact of single-residue mutations on protein thermal stability: The case of threonine 83 of BC2L-CN lectin

The thermal stability of trimeric lectin BC2L-CN was investigated and found to be considerably altered when mutating residue 83, originally a threonine, located at the fucose-binding loop. Mutants were analyzed using differential scanning calorimetry and isothermal microcalorimetry. Although most mutations decreased the affinity of the protein for oligosaccharide H type 1, six mutations increased the melting temperature (Tm) by >5 °C; one mutation, T83P, increased the Tm value by 18.2 °C(T83P, Tm = 96.3 °C). In molecular dynamic simulations, the investigated thermostable mutants, T83P, T83A, and T83S, had decreased fluctuations in the loop containing residue 83. In the T83S mutation, the side-chain hydroxyl group of serine formed a hydrogen bond with a nearby residue, suggesting that the restricted movement of the side-chain resulted in fewer fluctuations and enhanced thermal stability. Residue 83 is located at the interface and near the upstream end of the equivalent loop in a different protomer; therefore, fluctuations by this residue likely propagate throughout the loop. Our study of the dramatic change in thermal stability by a single amino acid mutation provides useful insights into the rational design of protein structures, especially the structures of oligomeric proteins.

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.

Simultaneous Enhancement of the Thermostability and Catalytic Activity of D-Allulose 3-Epimerase from Clostridium bolteae ATTC BAA-613 Based on the "Back to Consensus Mutations" Hypothesis

D-Allulose is a high value rare sugar with multiple physiological functions and commercial potential that can be enzymatically synthesized from D-fructose by D-allulose 3-epimerase (DAEase). Poor catalytic activity and thermostability of DAEase prevent the industrial production of D-allulose. In this work, rational design was applied to a previously identified DAEase from Clostridium bolteae ATCC BAA-613 based on the "back to consensus mutations" hypothesis, and the catalytic activity of the Cb-I265 V variant was enhanced 2.5-fold. Furthermore, the Cb-I265 V/E268D double-site variant displayed 2.0-fold higher specific catalytic activity and 1.4-fold higher thermostability than the wild-type enzyme. Molecular docking and kinetic simulation results indicated increased hydrogen bonds between the active pocket and substrate, possibly contributing to the improved thermal stability and catalytic activity of the double-site mutant. The findings outlined a feasible approach for the rational design of multiple preset functions of target enzymes simultaneously.

Structural and Functional Characterization of Obesumbacterium proteus Phytase: A Comprehensive In-Silico Study

Phytate, also known as myoinositol hexakisphosphate, exhibits anti-nutritional properties and possesses a negative environmental impact. Phytase enzymes break down phytate, showing potential in various industries, necessitating thorough biochemical and computational characterizations. The present study focuses on Obesumbacterium proteus phytase (OPP), indicating its similarities with known phytases and its potential through computational analyses. Structure, functional, and docking results shed light on OPP's features, structural stability, strong and stable interaction, and dynamic conformation, with flexible sidechains that could adapt to different temperatures or specific functions. Root Mean Square fluctuation (RMSF) highlighted fluctuating regions in OPP, indicating potential sites for stability enhancement through mutagenesis. The systematic approach developed here could aid in enhancing enzyme properties via a rational engineering approach. Computational analysis expedites enzyme discovery and engineering, complementing the traditional biochemical methods to accelerate the quest for superior enzymes for industrial applications.

Transporter mining and metabolic engineering of Escherichia coli for high-level D-allulose production from D-fructose by thermo-swing fermentation

D-Allulose is an ultra-low-calorie sweetener with broad market prospects in the fields of food, beverage, health care, and medicine. The fermentative synthesis of D-allulose is still under development and considered as an ideal route to replace enzymatic approaches for large-scale production of D-allulose in the future. Generally, D-allulose is synthesized from D-fructose through Izumoring epimerization. This biological reaction is reversible, and a high temperature is beneficial to the conversion of D-fructose. Mild cell growth conditions seriously limit the efficiency of producing D-allulose through fermentation. FryABC permease was identified to be responsible for the transport of D-allulose in Escherichia coli by comparative transcriptomic analysis. A cell factory was then developed by expression of ptsG-F, dpe, and deletion of fryA, fruA, manXYZ, mak, and galE. The results show that the newly engineered E. coli was able to produce 32.33 ± 1.33 g L-1 of D-allulose through a unique thermo-swing fermentation process, with a yield of 0.94 ± 0.01 g g-1 on D-fructose.

Optimization of Ultrahigh-Throughput Screening Assay for Protein Engineering of d-Allulose 3-Epimerase

d-Allulose is the corresponding epimer of d-fructose at the C-3 position, which exhibits a similar taste and sweetness to sucrose. As a low-calorie sweetener, d-allulose has broad application prospects in the fields of medicine, food, and so on. Currently, the production method of d-allulose is mainly the enzymatic conversion of d-fructose by d-allulose 3-epimerase (DAEase). However, the limited specific activity and thermal stability of DAEase restrict its industrial application. Herein, an ultrahigh-throughput screening assay based on the transcription factor PsiR was extensively optimized from the aspects of culture medium components, screening plasmid, and expression host, which enhanced the correction between the fluorescent readout and the enzyme activity. Then, the error-prone PCR (epPCR) library of Clostridium cellulolyticum H10 DAEase (CcDAEase) was screened through the above optimized method, and the variant I228V with improved specific activity and thermal stability was obtained. Moreover, after combining two beneficial substitutions, D281G and C289R, which were previously obtained by this optimized assay, the specific activity of the triple-mutation variant I228V/D281G/C289R reached up to 1.42-fold of the wild type (WT), while its half-life (T1/2) at 60 °C was prolonged by 62.97-fold. The results confirmed the feasibility of the optimized screening assay as a powerful tool for the directed evolution of DAEase.

Improving Both the Thermostability and Catalytic Efficiency of Phospholipase D from Moritella sp. JT01 through Disulfide Bond Engineering Strategy

Mining of Phospholipase D (PLD) with high activity and stability has attracted strong interest for investigation. A novel PLD from marine Moritella sp. JT01 (MsPLD) was biochemically and structurally characterized in our previous study; however, the short half-life time (t_1/2) under its optimum reaction temperature seriously hampered its further applications. Herein, the disulfide bond engineering strategy was applied to improve its thermostability. Compared with wild-type MsPLD, mutant S148C-T206C/D225C-A328C with the addition of two disulfide bonds exhibited a 3.1-fold t_1/2 at 35 °C and a 5.7 °C increase in melting temperature (T_m). Unexpectedly, its specific activity and catalytic efficiency (k_cat/K_m) also increased by 22.7% and 36.5%, respectively. The enhanced activity might be attributed to an increase in the activation entropy by displacing more water molecules by the transition state. The results of molecular dynamics simulations (MD) revealed that the introduction of double disulfide bonds rigidified the global structure of the mutant, which might cause the enhanced thermostability. Finally, the synthesis capacity of the mutant to synthesize phosphatidic acid (PA) was evaluated. The conversion rate of PA reached about 80% after 6 h reaction with wild-type MsPLD but reached 78% after 2 h with mutant S148C-T206C/D225C-A328C, which significantly reduced the time needed for the reaction to reach equilibrium. The present results pave the way for further application of MsPLD in the food and pharmaceutical industries.

Improved thermostability of D-allulose 3-epimerase from Clostridium bolteae ATCC BAA-613 by proline residue substitution

d-allulose, a rare sugar that is scarce in nature, exerts several beneficial effects and has commercial potential. d-allulose 3-epimerase (DAEase) plays a vital role in catalyzing the isomerization from d-fructose to d-allulose. However, the industrial application of DAEase for d-allulose production is hindered by its poor long-term thermostability. In the present research, we introduced a proline residue (i) to restrict its spatial conformation and (ii) to reduce the entropy of the unfolded state of DAEase. The t_1/2 value of the double-site Clostridium bolteae DAEase mutant Cb-51P/89P was prolonged to 58 min at 55 °C, a 2.32-fold increase compared with wild-type DAEase. The manipulation did not cause obvious changes in the enzymatic properties, including optimum pH, optimal temperature, optimum metal ion, and enzymatic activity. As the accumulation of multiple small effects through proline substitution could dramatically improve the thermostability of the mutant protein, our method to improve the thermostability while roughly retaining the original enzymatic properties is promising.

Computer-Aided Targeted Mutagenesis of Thermoclostridium caenicola d-Allulose 3-Epimerase for Improved Thermostability

d-Allulose 3-epimerase (DAEase) is a key enzyme in d-allulose bioproduction. DAEase from Thermoclostridium caenicola suffers from poor thermostability, hampering its large-scale applications in industry. In this study, mutants A70P, G107P, F155Y, and D162T with increased melting point temperature (T_m) were obtained by targeted mutagenesis based on the calculation of the free energy of folding. The optimal single-point mutant G107P showed 11.08 h, 5, and 5.70 °C increases in the values of half-life (t_1/2) at 60 °C, the optimum temperature (T_opt), and T_m, respectively. Beneficial mutations were combined by ordered recombination mutagenesis, and the combinational mutant Var3 (G107P/F155Y/D162T/A70P) was generated with ΔT_opt of 10 °C and ΔT_m of 12.25 °C. Its t_1/2 value at 65 °C was more than 140 times higher than that of the wild-type enzyme. Molecular dynamics simulations and homology modeling analysis indicated that the enhanced overall rigidity, increased hydrogen bonds between subunits, and redistributed surface electrostatic charges might be responsible for the improved thermostability of the mutant Var3.

Simultaneous improvement of the thermostability and activity of lactic dehydrogenase from Lactobacillus rossiae through rational design

d-Phenyllactic acid, is a versatile organic acid with wide application prospects in the food, pharmaceutical and material industries. Wild-type lactate dehydrogenase LrLDH from Lactobacillus rossiae exhibits a high catalytic performance in the production of d-phenyllactic acid from phenylpyruvic acid or sodium phenylpyruvate, but its industrial application is hampered by poor thermostability. Here, computer aided rational design was applied to improve the thermostability of LrLDH. By using HotSpot Wizard 3.0, five hotspot residues (N218, L237, T247, D249 and S301) were identified, after which site-saturation mutagenesis and combined mutagenesis were performed. The double mutant D249A/T247I was screen out as the best variant, with optimum temperature, t_1/2, and T¹⁰₅₀ that were 12 °C, 17.96 min and 19 °C higher than that of wild-type LrLDH, respectively. At the same time, the k_cat/K_m of D249A/T247I was 1.47 s⁻¹ mM⁻¹, which was 3.4 times higher than that of the wild-type enzyme. Thus rational design was successfully applied to simultaneously improve the thermostability and catalytic activity of LrLDH to a significant extent. The results of molecular dynamics simulations and molecular structure analysis could explain the mechanisms for the improved performance of the double mutant. This study shows that computer-aided rational design can greatly improve the thermostability of d-lactate dehydrogenase, offering a reference for the modification of other enzymes.

The d-LDH was engineered using computationally-assisted rational mutagenesis. The two mutants D249A and D249A/T247I showed significantly enhanced thermostability and catalytic activity to sodium phenylpyruvate compared with the wild-type enzyme.

D-allulose, a versatile rare sugar: recent biotechnological advances and challenges

D-Allulose is the C-3 epimer of D-fructose, and widely regarded as a promising substitute for sucrose. It's an excellent low-calorie sweetener, with 70% sweetness of sucrose, 0.4 kcal/g dietary energy, and special physiological functions. It has been approved as GRAS by the U.S. Food and Drug Administration, and is allowed to be excluded from total and added sugar counts on the food labels. Therefore, D-allulose gradually attracts more public attention. Owing to scarcity in nature, the bioproduction of D-allulose by using ketose 3-epimerase (KEase) has become the research hotspot. Herein, we give a summary of the physicochemical properties, physiological function, applications, and the chemical and biochemical synthesis methods of D-allulose. In addition, the recent progress in the D-allulose bioproduction using KEases, and the possible solutions for existing challenges in the D-allulose industrial production are comprehensively discussed, focusing on the molecular modification, immobilization, food-grade expression, utilizing low-cost biomass as feedstock, overcoming thermodynamic limitation, as well as the downstream separation and purification. Finally, Prospects for further development are also proposed.