Rational Design of Disulfide Bonds for Enhancing the Thermostability of the 1,4-α-Glucan Branching Enzyme from Geobacillus thermoglucosidans STB02

Rational Design Strategy to Improve the Thermal Stability of Alginate Lyase Pedsa0632

Alginate can be degraded by alginate lyase to produce alginate oligosaccharides (AOs). AOs are widely used in the food, agricultural, and pharmaceutical industries due to their various physiological activities. In this work, alginate lyase Pedsa0632 was successfully characterized, which exists in solution as monomers and oligomers. Pedsa0632 has poor thermal stability, displaying a half-life (t1/2, 55 °C) of merely 6.54 min at its optimum temperature. We attempted to improve the thermal stability of Pedsa0632 by changing the interface and increasing the content of the oligomers. A mutant library was generated through combinatorial engineering of disulfide bonds, intersubunit salt bridges, and PROSS (Protein Repair One-Stop Shop) guided stabilization strategies. Mutant L324 V-D353 V-M363T-T385 V (M3) was finally constructed. The wild-type (WT) enzyme was basically inactivated after 30 min of incubation at 55 °C, whereas M3 still maintained 60% relative activity after 11,000 min of incubation under the same conditions. Further structural comparisons between the WT and M3 revealed that the extraordinary stability of the M3 could be due to the mutation that induced a more stable and compact interface of Pedsa0632, resulting in an increased proportion of oligomer content. The rational design strategy used in this study can effectively improve the enzyme's thermal stability, especially oligomeric enzymes.

Warm irrigation fluid effect on Thulium fiber laser (TFL) ablation of uroliths

Prior laser studies have demonstrated that as the temperature of a medium increases, the amount of energy delivered to the target increases. We sought to investigate the role of irrigation fluid temperature on Thulium fiber laser (TFL) urolith ablation. 360 calculi were divided in vitro according to chemical composition: calcium oxalate monohydrate (COM), cystine (CYS), struvite (STR), calcium phosphate (CAP), uric acid (UA), and calcium oxalate dihydrate (COD). A 200 μm TFL was placed directly on each stone, while immersed in 0.9% NaCl at four different temperatures (25 C, 37 C, 44 C, 60 C) and a single laser pulse administered at distinct energy settings (0.1 J, 0.5 J, 1.5 J). Optical coherence tomography assessed the resulting ablation cone volume. Mean stone volume and porosity were evaluated through ANOVA and Tukey post-hoc analysis. A multivariate generalized model for each composition accounted for the impact of fluid temperature and laser energy on stone ablation. Warmer fluid temperatures yielded greater ablation cone volumes for most energy settings, excluding UA stones. When accounting for chemical composition, higher tensile strength stones (COM, CYS) benefited most from warmer fluid in comparison to frangible stones (CAP, STR). The effects of increasing fluid temperature are modest relative to laser pulse energy as a large temperature increase (i.e. 7ºC) is equivalent to a minor energy increase (i.e. 0.1 J). For non-UA stones, TFL ablation efficiency increases with warmer irrigation fluid. The effect, albeit modest compared to laser pulse energy, was most notable for COM and CYS stones.

Thermostability Enhancement of Tagatose 4-Epimerase through Protein Engineering and Whole-Cell Immobilization

d-Tagatose, a rare sugar endowed with a low-calorie property, superior taste quality, and probiotic functionality, has garnered significant research attention. However, the prevailing biological production methods relying on β-galactosidase and l-arabinose isomerase face challenges including high cost and suboptimal conversion efficiency. Consequently, it is of great research significance to find efficient alternative routes for d-tagatose synthesis. Previously, Thermotoga petrophila tagaturonate 3-epimerase was modified to function as tagatose 4-epimerase (T4E) enabling the direct conversion of d-fructose to d-tagatose. In this study, T4E was further engineered through directed evolution, specifically targeting the enhancement of its thermostability for application. This endeavor yielded promising T4E variants with superiority over those of the original enzyme. T4E I430P exhibits a half-life (t1/2) at 70 °C that is 1.83-fold that of T4E, with an increased melting temperature (Tm) of 5.1 °C compared to T4E. Additionally, T4E G90S/T272A/I430P demonstrated a 21.4% increase in specific activity compared to T4E. At 70 °C, its t1/2 was 1.69-fold that of T4E, and its Tm is 2.9 °C higher than T4E. Furthermore, whole-cell immobilization integrating these engineered T4E variants into a robust biocatalytic system was employed. This innovative approach not only underscores the practical feasibility of modifying enzymes through directed evolution but also establishes a foundation for the cost-effective, large-scale production of d-tagatose.

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.

ThermoLink: Bridging disulfide bonds and enzyme thermostability through database construction and machine learning prediction

Disulfide bonds, covalently formed by sulfur atoms in cysteine residues, play a crucial role in protein folding and structure stability. Considering their significance, artificial disulfide bonds are often introduced to enhance protein thermostability. Although an increasing number of tools can assist with this task, significant amounts of time and resources are often wasted owing to inadequate consideration. To enhance the accuracy and efficiency of designing disulfide bonds for protein thermostability improvement, we initially collected disulfide bond and protein thermostability data from extensive literature sources. Thereafter, we extracted various sequence- and structure-based features and constructed machine-learning models to predict whether disulfide bonds can improve protein thermostability. Among all models, the neighborhood context model based on the Adaboost-DT algorithm performed the best, yielding "area under the receiver operating characteristic curve" and accuracy scores of 0.773 and 0.714, respectively. Furthermore, we also found AlphaFold2 to exhibit high superiority in predicting disulfide bonds, and to some extent, the coevolutionary relationship between residue pairs potentially guided artificial disulfide bond design. Moreover, several mutants of imine reductase 89 (IR89) with artificially designed thermostable disulfide bonds were experimentally proven to be considerably efficient for substrate catalysis. The SS-bond data have been integrated into an online server, namely, ThermoLink, available at guolab.mpu.edu.mo/thermoLink.

Efficient Expression and Application of a Modified Rhizomucor miehei Lipase for Simultaneous Production of Biodiesel and Eicosapentaenoic Acid Ethyl Ester from Nannochloropsis Oil

Few reports exist on one-step enzymatic methods for the simultaneous production of biodiesel and eicosapentaenoic acid ethyl ester (EPA-EE), a high-value pharmaceutical compound. This study aimed to efficiently express Rhizomucor miehei lipase (pRML) in Pichia pastoris X-33 via propeptide mutation and high-copy strain screening. The mutated enzyme was then used to simultaneously catalyze the production of both biodiesel and EPA-EE. The P46N mutation in the propeptide (P46N-pRML) significantly boosted its production, with the four-copy strain increasing enzyme yield by 3.7-fold, reaching 3425 U/mL. Meanwhile, its optimal temperature increased to 45-50 °C, pH expanded to 7.0-8.0, specific activity doubled, Km reduced to one-third, and kcat/Km increased 7-fold. Notably, P46N-pRML efficiently converts Nannochloropsis gaditana oil's eicosapentaenoic acid (EPA). Under optimal conditions, it achieves up to 93% biodiesel and 92% EPA-EE yields in 9 h. Our study introduces a novel, efficient one-step green method to produce both biodiesel and EPA-EE using this advanced enzyme.

Improving the thermal stability and branching efficiency of Pyrococcus horikoshii OT3 glycogen branching enzyme

In practical applications, the gelatinisation temperature of starch is high. Most current glycogen branching enzymes (GBEs, EC 2.4.1.18) exhibit optimum activity at moderate or low temperatures and quickly lose their activity at higher temperatures, limiting the application of GBEs in starch modification. Therefore, we used the PROSS strategy combined with PDBePISA analysis of the dimer interface to further improve the heat resistance of hyperthermophilic bacteria Pyrococcus horikoshii OT3 GBE. The results showed that the melting temperature of mutant T508K increased by 3.1 °C compared to wild-type (WT), and the optimum reaction temperature increased by 10 °C for all mutants except V140I. WT almost completely lost its activity after incubation at 95 °C for 60 h, while all of the combined mutants maintained >40 % of their residual activity. Further, the content of the α-1,6 glycosidic bond of corn starch modified by H415W and V140I/H415W was approximately 2.68-fold and 1.92-fold higher than that of unmodified corn starch and corn starch modified by WT, respectively. Additionally, the glucan chains of DP < 13 were significantly increased in mutant modified corn starch. This method has potential for improving the thermal stability of GBE, which can be applied in starch branching in the food industry.

Conserved residues Glu and Phe at substrate binding groove of α-1,6-glucanases modulate branch of the product

Understanding what amino acids in α-1,6-glucanases target α-1,6 glycosidic bonds of polysaccharides is timely and important for generating products with branch structure. With this objective, we investigated 330 sequences from seven subfamilies to excavate amino acids for recognition or catalysis of α-1,6 glycosidic bonds. Computational analysis identified two amino acids, E343 and W521, trigger α-1,6 glycosidic bond specificity of enzymes. To explore the effect of E343 and W521 on the product structure, several engineered mutants were studied in our research. Product structural analysis showed that the ratio of amylose and amylopectin is obviously different. The catalytic mechanism revealed that the bulky aromatic side chain is a trigger that controls the ratio of branch glucans. The E148 acts as a proton donor to regulate the generation of branched structures in the product during transglycosidation of the glucan branching enzyme (GBE).

Rational Design of Disulfide Bridges in BbPETaseCD for Enhancing the Enzymatic Performance in PET Degradation

Polyethylene terephthalate (PET) is one of the most prevalent transparent thermoplastics. It is commonly utilized due to its low cost and high durability. With the massive accumulation of waste PET, however, serious environmental pollution has become a global problem. Compared to traditional chemical degradation, biodegradation of PET catalyzed by PET hydrolase (PETase) is more environmentally friendly and energy-efficient. BbPETase^CD from the Burkholderiales bacterium is a PETase that shows favorable properties for application in the biodegradation of PET. To enhance the enzymatic performance of this enzyme, this work focuses on the rational design of disulfide bridges in BbPETase^CD. We utilized two computational algorithms to predict the probable disulfide-bridge mutations in BbPETase^CD, and five variants were acquired from the computations. Among these, the N364C/D418C variant with one additional disulfide bond showed higher expression than the wild-type enzyme (WT) and the best enzymatic performance. The melting temperature (T_m) of the N364C/D418C variant presented an increase of 14.8 °C over that of WT (56.5 °C), indicating that the additional disulfide bond significantly raised the thermodynamic stability of the enzyme. Kinetic experiments at different temperatures also demonstrated the thermal stability increase of the variant. The variant also showed significantly increased activity over WT when using bis(hydroxyethyl) terephthalate (BHET) as the substrate. More remarkably, the N364C/D418C variant exhibited approximately an 11-fold increase over the WT enzyme in the long-term (14 days) degradation of PET films. The results prove that the rationally designed disulfide bond significantly improved the enzymatic performance of the enzyme for PET degradation.

Knotting terminal ends of mutant T1 lipase with disulfide bond improved structure rigidity and stability

Lipase biocatalysts offer unique properties which are often impaired by low thermal and methanol stability. In this study, the rational design was employed to engineer a disulfide bond in the protein structure of Geobacillus zalihae T1 lipase in order to improve its stability. The selection of targeted disulfide bond sites was based on analysis of protein spatial configuration and change of Gibbs free energy. Two mutation points (S2C and A384C) were generated to rigidify the N-terminal and C-terminal regions of T1 lipase. The results showed the mutant 2DC lipase improved methanol stability from 35 to 40% (v/v) after 30 min of pre-incubation. Enhancement in thermostability for the mutant 2DC lipase at 70 °C and 75 °C showed higher half-life at 70 °C and 75 °C for 30 min and 52 min, respectively. The mutant 2DC lipase maintained the same optimum temperature (70 °C) as T1 lipase, while thermally induced unfolding showed the mutant maintained higher rigidity. The kcat/Km values demonstrated a relatively small difference between the T1 lipase (WT) and 2DC lipase (mutant). The kcat/Km (s^-1 mM^-1) of the T1 and 2DC showed values of 13,043 ± 224 and 13,047 ± 312, respectively. X-ray diffraction of 2DC lipase crystal structure with a resolution of 2.04 Å revealed that the introduced single disulfide bond did not lower initial structural interactions within the residues. Enhanced methanol and thermal stability are suggested to be strongly related to the newly disulfide bridge formation and the enhanced compactness and rigidity of the mutant structure. KEY POINTS: • Protein engineering via rational design revealed relative improved enzymatic performance. • The presence of disulfide bond impacts on the rigidity and structural function of proteins. • X-ray crystallography reveals structural changes accompanying protein modification.

Biochemical characteristics and potential application of a thermostable starch branching enzyme from Bacillus licheniformis

Slowly digestible starch (SDS) has attracted increasing attention for its function of preventing metabolic diseases. Based on transglycosylation, starch branching enzymes (1,4-α-glucan branching enzymes, GBEs, EC 2.4.1.18) can be used to regulate the digestibility of starch. In this study, a GBE gene from Bacillus licheniformis (bl-GBE) was cloned, expressed, purified, and characterized. Sequence analysis and structural modeling showed that bl-GBE belong to the glycoside hydrolase 13 (GH13) family, with which its active site residues were conserved. The bl-GBE was highly active at 80 °C and a pH range of 7.5-9.0, and retained 90% of enzyme activity at 70 °C for 16 h. bl-GBE also showed high substrate specificity (80.88 U/mg) on potato starch. The stability and the changes of the secondary structure of bl-GBE at different temperature were determined by circular dichroism (CD) spectroscopy. The CD data showed a loss of 20% of the enzyme activity at high temperatures (80 °C), due to the decreased content of the α -helix in the secondary structure. Furthermore, potato starch treated with bl-GBE (300 U/g starch) showed remarkable increase in stability, solubility, and significant reduction viscosity. Meanwhile, the slowly digestible starch content of bl-GBE modified potato starch increased by 53.03% compared with native potato starch. Our results demonstrated the potential applications of thermophilic bl-GBE in food industries.

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

D-psicose 3-epimerase (DPEase) catalyzes the isomerization of D-fructose to D-psicose (aka D-allulose, a low-calorie sweetener), but its industrial application has been restricted by the poor thermostability of the naturally available enzymes. Computational rational design of disulfide bridges was used to select potential sites in the protein structure of DPEase from Clostridium bolteae to engineer new disulfide bridges. Three mutants were engineered successfully with new disulfide bridges in different locations, increasing their optimum catalytic temperature from 55 to 65 °C, greatly improving their thermal stability and extending their half-lives (t_1/2) at 55 °C from 0.37 h to 4−4.5 h, thereby greatly enhancing their potential for industrial application. Molecular dynamics simulation and spatial configuration analysis revealed that introduction of a disulfide bridge modified the protein hydrogen–bond network, rigidified both the local and overall structures of the mutants and decreased the entropy of unfolded protein, thereby enhancing the thermostability of DPEase.