High-temperature behavior of hyperthermostable Thermotoga maritima xylanase XYN10B after designed and evolved mutations

Enhancing the catalytic performance of xylanase XynASP through semi-rational design in the cord region to promote its application in juice clarification

In the GH11 family of xylanases, the cord region, a dynamic peptide linker connecting the "thumb" and "palm" regions, exhibits remarkable flexibility. To reveal the structure-function relationship in this region, saturation mutagenesis was performed on the cord segment of XynASP, a xylanase derived from Aspergillus saccharolyticus JOP 1030-1 GH11. Among the generated mutants, two variants, D116S and E119V, showed superior enzymatic properties and were subsequently combined to generate XynASP-SV. XynASP-SV exhibited a 3.05-fold increase in specific enzyme activity compared to the wild type, a 6 °C rise in Tm value, and a 4.62-fold extension in half-life at 50 °C. When beechwood xylan was used as the substrate, the kcat/Km of XynASP-SV increased 27.69-fold compared to the wild type. Molecular dynamics simulations revealed that the synergistic effects of the D116S and E119V mutations, along with amino acids in the "thumb" region, significantly enhanced the structural rigidity of XynASP-SV, thereby improving its thermostability. In the clarification experiments with mango and pitaya juices, XynASP-SV demonstrated substantial potential for industrial applications. This study highlights the enhanced catalytic performance of xylanase achieved by controlling its flexibility in the cord region.

Improving the Thermal Stability of GH11 Xylanase XynASP through Cord Region Engineering

The thermostability and catalytic activity of GH11 xylanase XynASP from Aspergillus saccharolyticus JOP 1030-1 were improved by systematically engineering the cord region. Ultimately, mutant DSM4 was developed through iterative combinations of mutations. Compared to the wild-type XynASP, DSM4 showed a 130.9- and 9.3-fold increase in t1/250 °C and catalytic efficiency, respectively. Reducing the flexibility of the cord region boosted the overall rigidity, resulting in improved thermal stability. The extensive catalytic cleft and prolonged contact between catalytic residues and the substrate were likely key factors in enhancing catalytic activity. Maintaining the thumb highly flexible can offset the negative impact on catalytic activity during the thermal stability modification of the cord region. This study indicates that the cord region is an effective target for enhancing the thermostability and catalytic activity of GH11 xylanase through engineered modifications.

Characterization and structural analysis of a leucine aminopeptidase using site-directed mutagenesis

Amp0279 (EC 3.4.11.24, GenBank: CP000817.1) is a Co2+-dependent leucine aminopeptidase from the Lysinibacillus sphaericus C3-41 genome. After analyses using molecular docking and spatial structure analysis, site-directed mutagenesis mutants were performed as Amp0279-R131E, Amp0279-R131H, Amp0279-R131A and Amp0279-E349D. The optimum pH of Amp0279-R131E was shifted from the original 8.5 to 7.5, and the overall electrostatic potential was shifted towards acidic. Compared with the original enzyme, the mutant proteins all gained better structural stability, especially the apparent melting temperature (Tm) of Amp0279-R131H increased from 41.8 to 45.5 °C. Morever, when protein was bound to the substrate, the Tm of Amp0279-R131E was increased by 7.3 °C and Amp0279-R131H increased by 5.4 °C, compared to the original enzyme. This is consistent with the results that the mutants acquired higher binding energies to the substrates, and an increase the hydrogen bonding force. In addition, the molecular docking of mutant and substrate revealed that the truncation of R131 contributes to the increase in the binding capacity of the substrate molecules to the active centre. In contrast, the presence of π-Cation interactions generated by R131 with the substrate has an important effect on the ability of Amp0279 to hydrolyse the substrate. This study demostrated that R131 is a key site for activity and stability, which is important in the future exploration of the functional structure of Amp0279.

Biofuel production from lignocellulose via thermophile-based consolidated bioprocessing

The depletion of fossil fuels and their impact on the environment have led to efforts to develop alternative sustainable fuels. While biofuel derived from lignocellulose is considered a sustainable, renewable, and green energy source, enhancing biofuel production and achieving a cost-effective bioconversion of lignocellulose at existing bio-refineries remains a challenge. Consolidated bioprocessing (CBP) using thermophiles can simplify this operation by integrating multiple processes, such as hydrolytic enzyme production, lignocellulose degradation, biofuel fermentation, and product distillation. This paper reviews recent developments in the conversion of lignocellulose to biofuel using thermophile-based CBP. First, advances in thermostable enzyme and thermophilic lignocellulolytic microorganism discovery and development for lignocellulosic biorefinery use are outlined. Then, several thermophilic CBP candidates and thermophilic microbes engineered to drive CBP of lignocellulose are reviewed. CRISPR/Cas-based genome editing tools developed for thermophiles are also highlighted. The potential applications of the Design-Build-Test-Learn (DBTL) synthetic biology strategy for designing and constructing thermophilic CBP hosts are also discussed in detail. Overall, this review illustrates how to develop highly sophisticated thermophilic CBP hosts for use in lignocellulosic biorefinery applications.

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.

qProtein: Exploring Physical Features of Protein Thermostability Based on Structural Proteomics

Thermostability, which is essential for the functional performance of enzymes, is largely determined by intramolecular physical interactions. Although many tools have been developed, existing computational methods have struggled to find the universal principles of protein thermostability. Recent advancements in structural proteomics have been driven by the introduction of deep neural networks such as AlphaFold2 and ESMFold. These innovations have enabled the characterization of protein structures with unprecedented speed and accuracy. Here, we introduce qProtein, a Python-implemented workflow designed for the quantitative analysis of physical interactions on the scale of structural proteomics. This platform accepts protein sequences as input and produces four structural features, including hydrophobic clusters, hydrogen bonds, electrostatic interactions, and disulfide bonds. To demonstrate the use of qProtein, we investigate the structural features related to protein thermostability in six glycoside hydrolase (GH) families, comprising a total of 3,811 protein structures. Our results indicate that in five enzyme families (GH11, GH12, GH5_2, GH10, and GH48), the thermophilic enzymes have a larger average area of hydrophobic clusters compared to the nonthermophilic enzymes within each family. Furthermore, our analysis of the local-structure regions reveals that the hydrophobic clusters are predominantly distributed in the distal regions of the GH11 enzymes. In addition, the average hydrophobic cluster area of the thermophilic enzymes is significantly higher than that of the nonthermophilic enzymes in the distal regions of the GH11 enzymes. Therefore, qProtein is a well-suited platform for analyzing the structural features of thermal stability at the level of structural proteomics. We provide the source code for qProtein at https://github.com/bj600800/qProtein, and the web server is available at http://qProtein.sdu.edu.cn:8888.

Simultaneously improving the activity and thermostability of hyperthermophillic pullulanase by modifying the active-site tunnel and surface lysine

Pullulanases are important starch-debranching enzymes that mainly hydrolyze the α-1,6-glycosidic linkages in pullulan, starch, and oligosaccharides. Nevertheless, their practical applications are constrained because of their poor activity and low thermostability. Moreover, the trade-off between activity and thermostability makes it challenging to simultaneously improve them. In this study, an engineered pullulanase was developed through reshaping the active-site tunnel and engineering the surface lysine residues using the pullulanase from Pyrococcus yayanosii CH1 (PulPY2). The specific activity of the engineered pullulanase was increased 3.1-fold, and thermostability was enhanced 1.8-fold. Moreover, the engineered pullulanase exhibited 11.4-fold improvement in catalytic efficiency (kcat/Km). Molecular dynamics simulations demonstrated an anti-correlated movement around the entrance of active-site tunnel and stronger interactions between the surface residues in the engineered pullulanase, which would be beneficial to the activity and thermostability improvement, respectively. The strategies used in this study and dynamic evidence for insight into enzyme performance improvement may provide guidance for the activity and thermostability engineering of other enzymes.

High-Throughput Screening Techniques for the Selection of Thermostable Enzymes

The acquisition of a thermostable enzyme is an indispensable prerequisite for its successful implementation in industrial applications and the development of novel functionalities. Various protein engineering approaches, including rational design, semirational design, and directed evolution, have been employed to enhance thermostability. However, all of these approaches require sensitive and reliable high-throughput screening (HTS) technologies to efficiently and rapidly identify variants with improved properties. While numerous reviews focus on modification strategies for enhancing enzyme thermostability, there is a dearth of literature reviewing HTS methods specifically aimed at this objective. Herein, we present a comprehensive overview of various HTS methods utilized for modifying enzyme thermostability across different screening platforms. Additionally, we highlight significant recent examples that demonstrate the successful application of these methods. Furthermore, we address the technical challenges associated with HTS technologies used for screening thermostable enzyme variants and discuss valuable perspectives to promote further advancements in this field. This review serves as an authoritative reference source offering theoretical support for selecting appropriate screening strategies tailored to specific enzymes with the aim of improving their thermostability.

Thr22 plays an important role in the efficient catalytic process of Bacillus subtilis chitosanase BsCsn46A

Threonine 22 (Thr22) located in catalytic center near the catalytic amino acid Glu19 was non-conserved in Bacillus species chitosanase. In order to study the function of Thr22, saturation mutagenesis was carried out towards P121N, a mutant previously constructed in our laboratory. Compared with P121N, which was designated as the wild type (WT) in this research, the specific enzyme activity of all mutants was decreased, and that of the T22P mutant was decreased by 91.6 %. Among these mutants, the optimum temperature decreased from 55 °C to 50 °C for 10 mutants and 45 °C for 4 mutants, respectively. The optimum temperature of mutant T22P was 40 °C. In order to analyze the reasons for the changes in enzymatic properties of the mutants, molecular docking analysis of WT and its mutants with substrate were performed. The hydrogen bond analysis around position 22 also conducted. The substitution of Thr22 was found to significantly affect the enzyme-substrate complex interaction. In addition, the hydrogen network near position 22 has undergone obvious changes. These changes may be the main reasons for the changes in enzymatic properties of the mutants. Altogether, this study is valuable for the future research on Bacillus chitosanase.

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.

A Novel Hyperthermostable Recombinant Protein Nanocage

Background

Background: Ferritin has an important role in iron storage in the cells, and due to its nanocage structure and self-assembly properties, it has wide application prospects in nanobiotechnology.

Methods

Methods: The maize (Zea mays) ferritin gene ZmFer1 was cloned and expressed in Escherichia coli BL21 (DE3) for the first time. Change in macromolecular structure of ZmFer1 ferritin due to heat treatment was investigated using native PAGE electrophoresis, dynamic light scattering (DLS), and transmission electron microscopy (TEM). Change in the secondary structures of the protein was evaluated using circular dichroism spectroscopy. Moreover, alteration in the conformation of the protein was evaluated using UV-absorption spectra and intrinsic fluorescence spectra. The melting temperature (Tm) of ZmFer1 was obtained using differential scanning calorimetry (DSC). Finally, the effect of heat on the function of ZmFer1 was assessed by iron loading ability.

Results

Results: The purified ZmFer1 protein showed a homopolymer nanocage structure. The results of native PAGE electrophoresis, DLS, and TEM techniques showed that ZmFer1 protein nanocage is stable to heat treatment up to 90 °C, and some of the protein nanocages retain their macromolecular structures even at 100 °C in liquid aqueous solution. Based on the DSC results, ZmFer1 protein nanocage had a Tm of 81.9 °C. After treatment at 100 °C, stable ZmFer1 protein nanocages were able to store iron atoms.

Conclusion

Conclusion: Recombinant ZmFer1 ferritin with a Tm > 80°C is a hyperthermostable protein nanocage. The results of this study are beneficial for the development of protein nanocages that are stable under extreme temperature conditions, as well as application of ZmFer1 in nanobiotechnology, biomaterials, and biomedical fields.