Machine learning-assisted substrate binding pocket engineering based on structural information.

Engineering enzyme-substrate binding pockets is the most efficient approach for modifying catalytic activity, but is limited if the substrate binding sites are indistinct. Here, we developed a 3D convolutional neural network for predicting protein-ligand binding sites. The network was integrated by DenseNet, UNet, and self-attention for extracting features and recovering sample size. We attempted to enlarge the dataset by data augmentation, and the model achieved success rates of 48.4%, 35.5%, and 43.6% at a precision of ≥50% and 52%, 47.6%, and 58.1%. The distance of predicted and real center is ≤4 Å, which is based on SC6K, COACH420, and BU48 validation datasets. The substrate binding sites of Klebsiella variicola acid phosphatase (KvAP) and Bacillus anthracis proline 4-hydroxylase (BaP4H) were predicted using DUnet, showing high competitive performance of 53.8% and 56% of the predicted binding sites that critically affected the catalysis of KvAP and BaP4H. Virtual saturation mutagenesis was applied based on the predicted binding sites of KvAP, and the top-ranked 10 single mutations contributed to stronger enzyme-substrate binding varied while the predicted sites were different. The advantage of DUnet for predicting key residues responsible for enzyme activity further promoted the success rate of virtual mutagenesis. This study highlighted the significance of correctly predicting key binding sites for enzyme engineering.

When biochar is involved in rhizosphere dissipation and plant absorption of pesticides: A meta-analysis.

Clarifying the influences of biochar input on the rhizosphere dissipation and plant absorption of pesticides is a crucial prerequisite for utilizing biochar in the restoration of pesticide-contaminated soils. Nevertheless, the application of biochar to pesticide-contaminated soils does not always achieve consistent results on the rhizosphere dissipation and plant absorption of pesticides. Under the new situation of vigorously promoting the application of biochar in soil management and carbon sequestration, a timely review is needed to further understand the key factors affecting biochar remediation of pesticide-contaminated soil. In this study, a meta-analysis was conducted utilizing variables from three dimensions of biochar, remediation treatment, and pesticide/plant type. The pesticide residues in soil and the pesticide uptake by plant were used as response variables. Biochar with high adsorption capacity can impede the dissipation of pesticides in soil and mitigate their absorption by plants. The specific surface area of biochar and the type of pesticide are critical factors that affect pesticide residues in soil and plant uptake, respectively. Applying biochar with high adsorption capacity, based on specific dosages and soil characteristics, is recommended for the remediation of continuously cultivated soil contaminated with pesticides. This article aims to provide a valuable reference and understanding for the application of biochar-based soil remediation technology and the treatment of pesticide pollution in soil.

Active secretion of a thermostable transglutaminase variant in Escherichia coli.

BACKGROUND: Streptomyces mobaraenesis transglutaminase (smTG) is widely used to generate protein crosslinking or attachment of small molecules. However, the low thermostability is a main obstacle for smTG application. In addition, it is still hard to achieve the secretory expression of active smTG in E. coli, which benefits the enzyme evolution. In this study, a combined strategy was conducted to improve the thermostability and secretory expression of active smTG in E. coli. RESULTS: First, the thermostable S. mobaraenesis transglutaminase variant S2P-S23V-Y24N-S199A-K294L (TGm1) was intracellularly expressed in pro-enzyme form in E. coli. Fusing the pro-region of Streptomyces hygroscopicus transglutaminase (proH) and TrxA achieved a 9.78 U/mL of intracellular smTG activity, 1.37-fold higher than the TGm1 fused with its native pro-region. After in vitro activation by dispase, the TGm1 with proH yielded FRAPD-TGm1, exhibiting 0.95 â„ƒ and 94.25% increases in melting temperature and half-life at 60 â„ƒ compared to FRAP-TGm1 derived from the expression using its native pro-region, respectively. Second, the TGm1 with proH was co-expressed with transglutaminase activating protease and chaperones (DnaK, DnaJ, and GrpE) in E. coli, achieving 9.51 U/mL of intracellular FRAPD-TGm1 without in vitro activation. Third, the pelB signal peptide was used to mediate the secretory expression of active TGm in E. coli, yielding 0.54 U/mL of the extracellular FRAPD-TGm1. A script was developed to shuffle the codon of pelB and calculate the corresponding mRNA folding energy. A 1.8-fold increase in the extracellular expression of FRAPD-TGm1 was achieved by the Top-9 pelB sequence derived from the coding sequences with the lowest mRNA folding energy. Last, deleting the gene of Braun's lipoprotein further increased the extracellular yield of FRAPD-TGm1 by 31.2%, reached 1.99 U/mL. CONCLUSIONS: The stabilized FRAPD-smTG here could benefit the enzyme application in food and non-food sectors, while the E. coli system that enables secretory expression of active smTG will facilitate the directed evolution for further improved catalytic properties. The combined strategy (N-terminal modification, co-expression with chaperones, mRNA folding energy optimization of signal peptide, and lipoprotein deletion) may also improve the secretory expression of other functional proteins in E. coli.

An Extensible Positioning System for Locating Mobile Robots in Unfamiliar Environments.

In this paper, an extensible positioning system for mobile robots is proposed. The system includes a stereo camera module, inertial measurement unit (IMU) and an ultra-wideband (UWB) network which includes five anchors, one of which is with the unknown position. The anchors in the positioning system are without requirements of communication between UWB anchors and without requirements of clock synchronization of the anchors. By locating the mobile robot using the original system, and then estimating the position of a new anchor using the ranging between the mobile robot and the new anchor, the system can be extended after adding the new anchor into the original system. In an unfamiliar environment (such as fire and other rescue sites), it is able to locate the mobile robot after extending itself. To add the new anchor into the positioning system, a recursive least squares (RLS) approach is used to estimate the position of the new anchor. A maximum correntropy Kalman filter (MCKF) which is based on the maximum correntropy criterion (MCC) is used to fuse data from the UWB network and IMU. The initial attitude of the mobile robot relative to the navigation frame is calculated though comparing position vectors given by a visual simultaneous localization and mapping (SLAM) system and the UWB system respectively. As shown in the experiment section, the root mean square error (RMSE) of the positioning result given by the proposed positioning system with all anchors is 0.130 m. In the unfamiliar environment, the RMSE is 0.131 m which is close to the RMSE (0.137 m) given by the original system with a difference of 0.006 m. Besides, the RMSE based on Euler distance of the new anchor is 0.061 m.

Effects of activated carbon, biochar, and carbon nanotubes on the heterogeneous Fenton oxidation catalyzed by pyrite for ciprofloxacin degradation.

Pyrite and engineering carbon materials have received increasing attention for their catalytic potential in Fenton reactions due to their extensive sources and low cost. However, effects of carbon materials on the degradation of pollutants by pyrite-catalyzed heterogeneous Fenton oxidation have not been fully understood. In this study, the performance of pyrite-catalyzed heterogeneous Fenton system on the degradation of ciprofloxacin (CIP) was investigated in the presence of activated carbon (AC), biochar (BC), and carbon nanotubes (CNTs). Synchronous and asynchronous experiments (adsorption and catalysis) were conducted to elucidate the roles of the carbon materials in pyrite-catalyzed Fenton reactions. The results demonstrated that all the three carbon materials accelerated the pyrite-catalyzed Fenton oxidation of CIP. Under the experimental conditions, the reaction rates, which were obtained by fitting the synchronous experimental results with the pseudo-first-order kinetic model, of pyrite/AC, pyrite/BC and pyrite/CNTs with H2O2 for the removal of CIP were 8.28, 3.40 and 3.37 times faster than that of pyrite alone. Adsorption experiments and characterization analysis showed that AC had a higher adsorption capacity than BC and CNTs for CIP, which enabled it to distinguish itself in assisting the pyrite-catalyzed Fenton oxidation. In the presence of the carbon materials, the adsorption effect should not be neglected when studying the catalytic performance of pyrite. Free radical quenching experiments and electron spin-resonance spectroscopy (ESR) were used to detect and identify free radical species in the reactions. The results showed that hydroxyl radicals (•OH) contributed significantly to the degradation of CIP. The addition of carbon materials promoted the production of •OH, which favored the degradation of CIP. The results of this study suggested that the synergistic effect of oxidation and adsorption promoted the removal of CIP in pyrite/carbon materials/H2O2 systems, and coupling pyrite and carbon materials shows great potential in treating antibiotic wastewater.

Significantly Improving the Thermostability and Catalytic Efficiency of Streptomyces mobaraenesis Transglutaminase through Combined Rational Design.

Streptomyces mobaraenesis transglutaminase has been widely used in food processing. We here significantly improved the catalytic properties of S2P-S23V-Y24N-S199A-K294L (TGm1), a highly stabilized variant of the transglutaminase. First, a virtual proline scan was performed based on folding free energy changes to obtain TGm1 variants with enhanced thermostability. Second, the residues within 15 Å of Cys64 in the enzyme-substrate complex of TGm1 were subjected to virtual saturation mutagenesis to generate the variants with reduced binding free energy and increased activity. After combining the favorable mutations, we obtained the variant FRAPD-TGm1-E28T-A265P-A287P (FRAPD-TGm2), exhibiting 66.9 min of half-life at 60 °C (t1/2(60 °C)), 67.8 °C of melting temperature (Tm), and 71.8 U/mg of specific activity, which are 2-fold, 2.6 °C, and 43.8% higher than those of FRAPD-TGm1, respectively. At last, to increase the surface negative net charge of FRAPD-TGm2, we introduced the mutations N96E-S144E-N163D-R183E-R208E-K325E, yielding FRAPD-TGm3. The latter's t1/2(60 °C), Tm, and specific activity were 122.9 min, 68.6 °C, and 83.7 U/mg, which are 83.8%, 0.8 °C, and 16.6% higher than the former, respectively. FRAPD-TGm3 is thus a robust candidate for transglutaminase application.