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Streptomyces mobaraensis transglutaminase (smTG) has been widely used in the food processing industry for protein crosslinking. However, its poor thermostability becomes a major obstacle to further applications. It is significant to develop a feasible strategy to improve the thermostability of smTG. Here, we developed a computational model based on the Siamese graph neural network framework to identify residues critical to the thermostability of smTG by predicting changes in folding free energy (ΔΔG) between the wild type and mutants. Four candidate residues were selected for mutation experiments, and the single mutant H44C exhibited 2.7 U mg−1 residual enzyme activity after 10 min incubation at 60 °C, twice as much as the wild type. Mutants Q74F and E87W also exhibited 3- and 2.3-times greater activity after 20 min. Molecular dynamics (MD) simulations revealed that smTG mutants (H44C, Q74F, and E87W) improved thermostability by enhancing hydrogen bond interactions, increasing additional residue interactions, and reducing loop flexibility. The MM-GBSA calculation demonstrated that mutants H44C and Q74F enhanced binding affinity with the substrate, and six residues crucial for substrate binding were identified. This study combines computational analysis with mutation assays for the rational design of smTG and offers a facile and efficient strategy to understand and improve the thermostability of proteins for industrial applications. [ABSTRACT FROM AUTHOR]

Objective: To study structure-specific solubilization effect of Sulfobutyl ether-β-cyclodextrin (SBE-β-CD) on Remdesivir (RDV) and to understand the experimental clathration with the aid of quantum mechanics (QM), molecular docking and molecular dynamics (MD) calculations. Methods: The experiment was carried out by phase solubility method at various pH and temperatures, while the concentration of Remdesivir in the solution was determined by HPLC. The complexation mechanism and the pH dependence of drug loading were investigated following a novel procedure combining QM, MD and molecular docking, based on accurate pKa predictions. Results: The phase solubility and solubilization effect of RDV in SBE-β-CD were explored kinetically and thermodynamically for each assessed condition. An optimal drug / SBE-β-CD feeding molar ratio was determined stoichiometrically for RDV solubility in pH1.7 solution. The supersaturated solubility was examined over time after pH of the solution was adjusted from 1.7 to 3.5. A possible hypothesis was raised to elucidate the experimentally observed stabilization of supersaturation based on the proposed RDV Cation A /SBE-β-CD pocket conformations. Conclusion: The computational explorations conformed to the experimentally determined phase solubilization and well elucidated the mechanism of macroscopic clathration between RDV and SBE-β-CD from the perspective of microscopic molecular calculations. [ABSTRACT FROM AUTHOR]

Chinese rural domestic waste has increased considerably with the modernization of agriculture and urbanization. Pyrolysis gasification is a common high-temperature waste treatment method. However, this method is usually accompanied by a large amount of particle emission. In this study, a rural domestic waste pyrolysis gasification station in Gansu Province, Northwest China, was selected for research. The particle emission characteristics of this station were analyzed, and the results showed that the original particle removal technologies were inefficient in fine particles. Hence, a new method of fine particle treatment, i.e., Cloud-Air-Purifying (CAP) technology, was explored herein. In CAP, fine particles grow in size via heterogeneous condensation in a supersaturated water vapor environment and are then collected efficiently using a supergravity field. A laboratory-scale pyrolysis gasifier and CAP equipment were built. Moreover, the CAP removal efficiency for particles generated from four typical rural domestic waste categories was studied. The results showed that CAP technology considerably increased the efficiency of fine particle removal. However, the removal efficiency for particles released owing to the incineration of wood was only ∼75%. This was because the tar substances formed during wood pyrolysis were attached to the surface of escaping particles, which led to a decrease in their hydrophilicity and particle condensation growth. To address this issue, the improvement in particle hydrophilicity using different surfactants was studied via molecular dynamic simulations. When the increase in water molecule adsorption, surface polarity, and the solid–liquid interaction energy for different surfactants were compared, alkylphenol ethoxylate (OP10) proved to be the most effective surfactant. Finally, the improved CAP technology combined with OP10 was applied to the on-site pyrolysis gasification flue gas treatment. Long term monitoring of the proposed technology revealed that particle removal efficiency remained >94%, exhibiting excellent fine particle removal. The successful application of the proposed technology demonstrates its potential for further application. • Pyrolysis gasification generates micron-sized fine particles and tar substances. • CAP technology contributes to size growth and removal of small sized particles. • Attachment of tar substances reduces the hydrophilicity of particles. • MD simulations proves that surfactants can enhance the particle hydrophilicity. [ABSTRACT FROM AUTHOR]

Abstract Single-layer molybdenum disulfide (MoS 2) is a novel two-dimensional material that has attracted considerable attention because of its excellent properties. In this work, molecular dynamics simulations were performed to investigate the effect of different kinds of alkali metal ions (Li+, Na+, and K+) on the flow resistance of ionic aqueous solutions confined in MoS 2 nanoslits under shearing. Three slit widths (i.e. 1.2, 1.6, and 2.0 nm) were investigated. Simulation results showed that the friction coefficient followed the order of K+ < Na+ < Li+. The friction coefficient decreased with the increasing of slit width. Unique confined spatial distributions of different types of ionic aqueous solutions led to different confined ionic hydrations for different cations. These differences lead to different orientations of surrounding water molecules and then form different hydrogen bond (HB) networks. The friction coefficient was greatly dependent on the number of HBs per water; i.e. , the larger the number of HBs formed, the lower was the flow resistance. Graphical abstract Image 1 [ABSTRACT FROM AUTHOR]

The confinement of titanium dioxide (TiO 2 ) significantly affects the nanoconfined water molecules behaviors, manifested structurally as fluid layering and dynamically as slowing down of fluid mobility near the confining surface. In this work, we carried out molecular dynamics simulations to investigate temperature-dependent structural characteristics of water molecules confined in rutile (110) nanoslits. Specifically, we studied the microstructure of two layers of water molecules near TiO 2 surface under temperatures ranging from 27 to 800 °C. The simulation results showed that the mean residence time of the first layer of water molecules decreased with temperature. A dramatic decreasing rate occurred when the temperature went beyond 300 °C. Detailed microstructural investigation of confined water molecules showed that with the increase of temperature, the orientation of some water molecules changed. The possible reason is that water molecules obtained more kinetic energy due to the higher interfacial temperature, so as to increase the probability of forming hydrogen bonds between water molecules in layer I. Moreover, dimers of water molecules, which exhibit higher mobility than water monomers near TiO 2 surfaces, began to form at about 300 °C. The formation of hydrogen bonds within the first layer of water molecules is largely responsible for the reduction of mean residence time. The results of this work provide perceptive guidelines for the application of TiO 2 at high temperatures, such as TiO 2 -supported catalysts. [ABSTRACT FROM AUTHOR]

Various nanotube- and graphene-based materials have been used in a wide range of applications associated with nanoconfined ions and these nanomaterial designers aim to learn more about the underlying mechanisms of ion behaviour at the nanoscale through molecular simulation. In the present work, we summarised recent progress of molecular simulation studies on the nanoconfined ionic transport behaviour in aqueous solutions. With regard to nanomaterial design, the significance of molecular simulation studies and the derived important design principles were selectively highlighted in three major applications, including separation based on nanoporous membranes, electrochemical-related energy storage and DNA nanopore sequencing. Molecular simulation evaluations of influencing factors were also reviewed based on ionic hydration and ion pairing under nanoconfinement, which primarily contribute to ionic transport. Moreover, we also discussed useful analysis methods based on the microscopic molecular dynamics trajectory information for improved evaluation of the microscopic properties of the nanoporous material towards different applications. [ABSTRACT FROM AUTHOR]

Using external stimuli to control ionic transport behavior in nanopores is an important focus of nanodevice research allowing numerous potential applications. A novel strategy was investigated to control ionic-transport resistance responses to the electric field intensity in a nanopore and regulate ionic selectivity. Molecular simulations were performed to examine the transport behaviors of K+ and Na+ in a carbon nanotube-based biomimetic nanopore under different electric fields. The responses of the modified group to the electric field intensity induced variations in ionic transport resistance, which then led to improved ionic selectivity. This result indicates that driving force and resistance are simultaneously affected by external stimuli under nanoconfinement. [ABSTRACT FROM AUTHOR]

Choline chloride/urea (1:2) is the most widely used deep eutectic solvent, which has attracted much attention due to its excellent advantages of low cost, environment friendly and easy synthesis. In this work, nanofriction-based molecular dynamics simulations were performed to investigate the effect of interfacial hydrophilicity on the flow resistance of Choline chloride/urea (1:2) confined in ionic model nanoslits. Simulation results showed that the flow resistance of the choline chloride/urea system increases with the increasing interfacial hydrophilicity. Urea molecules form a preferential adsorption layer on the wall. As the interfacial hydrophilicity increases, the number of urea molecules in the interfacial adsorption layer increased, whereas the stability decreased. Unique confined spatial distributions of urea molecules greatly contribute to ionic association between choline cations and chloride anions. Furthermore, with the increase of interfacial hydrophilicity, orientation distributions of urea molecules in the adsorption layer are more orderly, then causing a decrease in the average hydrogen bond number (N HB) of urea molecules. Moreover, the more the N HB of urea molecules, the better is the stability in the interfacial adsorption layer, which in turn results in less flow resistance. [ABSTRACT FROM AUTHOR]

Residual Ca2+ decreases the efficiency and increases the power consumption of the chlor-alkali industry. However, Ca2+ and Na+ sieving is challenging due to the similar ionic radii of these cations. Inspired by the presence of carbonyl oxygens in key selective filters of biological Ca2+ and Na+ channels, we used molecular dynamics to investigate the effects of carbonyl oxygen atoms in modified graphene nanopores of various sizes (characteristic diameters: 0.57–1.50 nm) on Ca2+/Na+ sieving. The results demonstrated that selectivity is closely associated with the different roles of the carbonyl oxygen atoms. In small nanopores, Ca2+ sheds increased numbers of water molecules due to the predominant steric effect of carbonyl oxygen atoms. Thus, Ca2+ must overcome a higher energy barrier than Na+. This requirement prevents the passage of Ca2+. In large nanopores, carbonyl oxygen atoms do preferentially substitute water molecules outside the first hydration shell of Ca2+ compared with those outside the first hydration shell of Na+, thereby hindering Na+ departure from the nanopore. These findings provide useful guidance for the further development of Ca2+ separation materials as sensors and ion separators. Image 1 [ABSTRACT FROM AUTHOR]

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