Improving the Catalytic Activity and Thermostability of MAS1 Lipase by Alanine Substitution

Homology modeling and thermostability enhancement of Vibrio palustris PETase via hydrophobic interactions

The quest for sustainable solutions to plastic pollution has driven research into plastic-degrading enzymes, offering promising avenues for polymer recycling applications. However, enzymes derived from natural sources often exhibit suboptimal thermostability, hindering their industrial viability. Protein engineering techniques have emerged as a powerful approach to enhance the desired properties of these biocatalysts. This study aims to conduct a comprehensive analysis of the thermostability of Vibrio palustris PETase (VpPETase) through an integrated computational approach encompassing homology modeling, site-specific molecular docking, molecular dynamics (MD) simulations, and comparative evaluation of a single-point mutation (V195F) against the wild-type enzyme. Homology modeling was used to predict VpPETase model using multiple templates. Model quality was rigorously assessed using Ramachandran plot analysis, ProSA, Verify 3D, and ERRAT. Molecular docking elucidated the catalytic region comprising residues His149, Asp117, and Ser71, while highlighting the pivotal roles of His149, Tyr1, and Ser71 in substrate binding affinity. MD simulations at various temperatures revealed higher stability at 313.15 K over a 100 ns trajectory, as evidenced by analyses of root-mean-square deviation (RMSD), radius of gyration (Rg), solvent-accessible surface area (SASA), hydrogen bonding, and root-mean-square fluctuation (RMSF). The V195F mutant exhibited a slight increase in stability compared to wild-type. While this study provides valuable insights into the thermostability of VpPETase, further investigations, including experimental validation of thermostability enhancements and in vitro characterization, are warranted to fully exploit the potential of this enzyme for industrial applications in plastic recycling.

Enhancing Stability and Catalytic Activity of d-Allulose 3-Epimerase through Multistrategy Computational Design and Cross-Regional Advantageous Mutations

d-Allulose 3-epimerase (DAEase) derived from Clostridium bolteae has excellent properties in the catalytic production of d-allulose, a rare sugar with unique biological functions. However, the industrial application of C. bolteae DAEase (Cb-DAEase) for d-allulose production is hindered by its low enzyme activity, poor long-term thermostability, and pH tolerance. In this study, we identified potential noncatalytic residues in Cb-DAEase using methods such as proline substitution, surface charge engineering, and surface residue prediction. The effects of these residues were experimentally validated, followed by structural analysis, which led to the generation of multisite mutants through cross-regional structural combinations. The obtained mutant Cb-R2P-E6P-D137C showed 155.6% of the enzyme activity of the wild type, and the Kcat/Km increased by 1.3-fold, an elevated half-life of 15.7 min, and an elevated Tm value of 1.1 °C. The mutant Cb-R2P-E6P-A83D-D137C had 139.7% of the enzyme activity of the wild type, the Kcat/Km increased by 1.2-fold, with an elevated half-life of 12.3 min, an elevated Tm value of 0.8 °C, and maintained 68% of the enzyme activity at pH 5.0. The findings outlined a feasible approach for the rational design of multiple preset functions of target enzymes simultaneously.

Current status and emerging frontiers in enzyme engineering: An industrial perspective

Protein engineering mechanisms can be an efficient approach to enhance the biochemical properties of various biocatalysts. Immobilization of biocatalysts and the introduction of new-to-nature chemical reactivities are also possible through the same mechanism. Discovering new protocols that enhance the catalytic active protein that possesses novelty in terms of being stable, active, and, stereoselectivity with functions could be identified as essential areas in terms of concurrent bioorganic chemistry (synergistic relationship between organic chemistry and biochemistry in the context of enzyme engineering). However, with our current level of knowledge about protein folding and its correlation with protein conformation and activities, it is almost impossible to design proteins with specific biological and physical properties. Hence, contemporary protein engineering typically involves reprogramming existing enzymes by mutagenesis to generate new phenotypes with desired properties. These processes ensure that limitations of naturally occurring enzymes are not encountered. For example, researchers have engineered cellulases and hemicellulases to withstand harsh conditions encountered during biomass pretreatment, such as high temperatures and acidic environments. By enhancing the activity and robustness of these enzymes, biofuel production becomes more economically viable and environmentally sustainable. Recent trends in enzyme engineering have enabled the development of tailored biocatalysts for pharmaceutical applications. For instance, researchers have engineered enzymes such as cytochrome P450s and amine oxidases to catalyze challenging reactions involved in drug synthesis. In addition to conventional methods, there has been an increasing application of machine learning techniques to identify patterns in data. These patterns are then used to predict protein structures, enhance enzyme solubility, stability, and function, forecast substrate specificity, and assist in rational protein design. In this review, we discussed recent trends in enzyme engineering to optimize the biochemical properties of various biocatalysts. Using examples relevant to biotechnology in engineering enzymes, we try to expatiate the significance of enzyme engineering with how these methods could be applied to optimize the biochemical properties of a naturally occurring enzyme.

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.

A Novel Lipase from Streptomyces exfoliatus DSMZ 41693 for Biotechnological Applications

Genome mining of Streptomyces exfoliatus DSMZ 41693 has allowed us to identify four different lipase-encoding sequences, and one of them (SeLipC) has been successfully cloned and extracellularly expressed using Rhodococcus sp. T104 as a host. SeLipC was purified by one-step hydrophobic interaction chromatography. The enzyme is a monomeric protein of 27.6 kDa, which belongs to subfamily I.7 of lipolytic enzymes according to its phylogenetic analysis and biochemical characterization. The purified enzyme shows the highest activity at 60 °C and an optimum pH of 8.5, whereas thermal stability is significantly improved when protein concentration is increased, as confirmed by thermal deactivation kinetics, circular dichroism, and differential scanning calorimetry. Enzyme hydrolytic activity using p-nitrophenyl palmitate (pNPP) as substrate can be modulated by different water-miscible organic cosolvents, detergents, and metal ions. Likewise, kinetic parameters for pNPP are: KM = 49.6 µM, kcat = 57 s-1, and kcat/KM = 1.15 × 106 s-1·M-1. SeLipC is also able to hydrolyze olive oil and degrade several polyester-type polymers such as poly(butylene succinate) (PBS), poly(butylene succinate)-co-(butylene adipate) (PBSA), and poly(ε-caprolactone) (PCL). Moreover, SeLipC can catalyze the synthesis of different sugar fatty acid esters by transesterification using vinyl laurate as an acyl donor, demonstrating its interest in different biotechnological applications.

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.

Molecular mechanism of LIP05 derived from Monascus purpureus YJX-8 for synthesizing fatty acid ethyl esters under aqueous phase

Fatty acid ethyl esters are important flavor chemicals in strong-flavor Baijiu. Monascus purpureus YJX-8 is recognized as an important microorganism for ester synthesis in the fermentation process. Enzyme LIP05 from YJX-8 can efficiently catalyze the synthesis of fatty acid ethyl esters under aqueous phase, but the key catalytic sites affecting esterification were unclear. The present work combined homology modeling, molecular dynamics simulation, molecular docking and site-directed mutation to analyze the catalytic mechanism of LIP05. Protein structure modeling indicated LIP05 belonged to α/β fold hydrolase, contained a lid domain and a core catalytic pocket with conserved catalytic triad Ser150-His215-Asp202, and the oxyanion hole composed of Gly73 and Thr74. Ile30 and Leu37 of the lid domain were found to affect substrate specificity. The π-bond stacking between Tyr116 and Tyr149 played an important role in stabilizing the catalytic active center of LIP05. Tyr116 and Ile204 determined the substrate spectrum by composing the substrate-entrance channel. Residues Leu83, Ile204, Ile211 and Leu216 were involved in forming the hydrophobic substrate-binding pocket through steric hindrance and hydrophobic interaction. The catalytic mechanism for esterification in aqueous phase of LIP05 was proposed and provided a reference for clarifying the synthesis of fatty acid ethyl esters during the fermentation process of strong-flavor Baijiu.

Integrated Utilization Strategy for Soybean Oil Deodorizer Distillate: Synergically Synthesizing Biodiesel and Recovering Bioactive Compounds by a Combined Enzymatic Process and Molecular Distillation

Soybean oil deodorizer distillate (SODD) is well recognized as a good source of both biodiesel and high-value bioactive compounds of tocopherols, squalene, and phytosterols. To achieve a one-step synthesis of biodiesel and recovery of bioactive compounds from SODD, four commercial immobilized enzymes (Novozym 435, Lipozyme TLIM, Lipozyme RMIM, and Lipozyme RM) and one self-prepared immobilized lipase MAS1-H108A were compared. The results showed that immobilized lipase MAS1-H108A due to the better methanol tolerance and higher catalytic activity gave the highest biodiesel yield of 97.08% under the optimized conditions: molar ratio of 1:2 (oil/methanol), temperature of 35 °C, and enzyme loading of 35 U/g SODD, even after 10 persistent cycles without significant decrease of activity. Simultaneously, there was no loss of tocopherols and squalene in SODD during the enzymatic reaction. Pure biodiesel (characterized by fourier transform infrared (FT-IR) and nuclear magnetic resonance (NMR)) and a high concentration of bioactive compounds could be successfully separated by molecular distillation at 100 °C. In a word, this work provides an interesting idea to achieve environmentally friendly treatment of SODD by combining an enzymatic process and molecular distillation, and it is suitable for industrial production.

Enzyme engineering and its industrial applications

Recently, there has been an increase in the demand for enzymes with modified activity, specificity, and stability. Enzyme engineering is an important tool to meet the demand for enzymes adjusted to different industrial processes. Knowledge of the structure and function of enzymes guides the choice of the best strategy for engineering enzymes. Each enzyme engineering strategy, such as rational design, directed evolution, and semi-rational design, has specific applications, as well as limitations, which must be considered when choosing a suitable strategy. Engineered enzymes can be optimized for different industrial applications by choosing the appropriate strategy. This review features engineered enzymes that have been applied in food, animal feed, pharmaceuticals, medical applications, bioremediation, biofuels, and detergents.

Properties of immobilized MAS1-H108A lipase and its application in the efficient synthesis of n-3 PUFA-rich triacylglycerols

This study reports the properties of immobilized MAS1-H108A lipase from marine Streptomyces sp. strain W007 on XAD1180 resin and its application in the synthesis of n-3 polyunsaturated fatty acids (PUFA)-rich triacylglycerols (TAG) for the first time. It was found that the optimal temperature and pH for both immobilized MAS1-H108A lipase and free lipase MAS1-H108A were 70 °C and 7.0, respectively. However, immobilized MAS1-H108A lipase exhibited higher thermostability when compared with free lipase MAS1-H108A. It was also interesting that both immobilized MAS1-H108A lipase and free lipase MAS1-H108A showed no regiospecificity in the hydrolysis of triolein. Subsequently, immobilized MAS1-H108A lipase and free lipase MAS1-H108A were employed to catalyze glycerolysis of n-3 PUFA-rich ethyl esters (EE) and esterification of n-3 PUFA with glycerol under vacuum in the solvent-free system. The results showed that n-3 PUFA-rich TAG were synthesized efficiently by non-regiospecific immobilized MAS1-H108A lipase and TAG contents separately reached 92.07% and 76.13% during the esterification and glycerolysis reactions, which were significantly higher than those (71.82% and 39.62%, respectively) obtained by free lipase MAS1-H108A. Besides, TAG exhibited similar n-3 PUFA composition to the substrate. These findings indicated that non-regiospecific immobilized MAS1-H108A lipase is a promising and efficient biocatalyst for the industrial synthesis of n-3 PUFA-rich TAG.

Recent advances in high-throughput mass spectrometry that accelerates enzyme engineering for biofuel research

Enzymes play indispensable roles in producing biofuels, a sustainable and renewable source of transportation fuels. Lacking rational design rules, the development of industrially relevant enzyme catalysts relies heavily on high-throughput screening. However, few universal methods exist to rapidly characterize large-scale enzyme libraries. Therefore, assay development is necessary on an ad hoc basis to link enzyme properties to spectrophotometric signals and often requires the use of surrogate, optically active substrates. On the other hand, mass spectrometry (MS) performs label-free enzyme assays that utilize native substrates and is therefore generally applicable. But the analytical speed of MS is considered rate limiting, mainly due to the use of time-consuming chromatographic separation in traditional MS analysis. Thanks to new instrumentation and sample preparation methods, direct analyte introduction into a mass spectrometer without a prior chromatographic step can be achieved by laser, microfluidics, and acoustics, so that each sample can be analyzed within seconds. Here we review recent advances in MS platforms that improve the throughput of enzyme library screening and discuss how these advances can potentially facilitate biofuel research by providing high sensitivity, selectivity and quantitation that are difficult to obtain using traditional assays. We also highlight the limitations of current MS assays in studying biofuel-related enzymes and propose possible solutions.