Enzyme is stabilized by a protection layer of ionic liquids in supercritical CO2: Insights from molecular dynamic simulation

Deep eutectic solvent combined with soybean as an efficient approach to enhance the content of apigenin in the Chrysanthemum indicum L. extract

Our research aimed to cost-effectively enhance apigenin content in Chrysanthemum indicum L. extract using soybeans combined with a deep eutectic solvent. First, various deep eutectic solvents were investigated for the extraction of apigenin, followed by soybean treatment to increase aglycon levels. Combining single factor experiments with response surface methodology and optimization algorithms (genetic algorithm and particle swarm optimization), the optimal conditions were also determined. The results revealed that choline chloride-propylene glycol emerged as the optimal solvent. The optimized treatment conditions involved a temperature of 54 °C, a time of 2 h, and the addition of 3 mL of soybean extract, yielding an apigenin content of 3.380 ± 0.031 mg/g - a remarkable eightfold increase compared to the initial extract. The computational study suggested that the deep eutectic solvent may play an important role in stabilizing β-glucosidase in soybeans. However, further research is needed to scale up and fully elucidate soybean's mechanism.

Molecular mechanism of cellulose dissolution in N-methyl morpholine-N-oxide: A molecular dynamics simulation study

N-methyl morpholine-N-oxide (NMMO) is the only commercialised solvent to dissolve cellulose and produce lyocell. However, the molecular mechanism of NMMO-induced cellulose solubilisation is unknown which limits further process development. In this work, and for the first time the complete dissolution process of a large cellulose bunch was simulated in NMMO monohydrate using long microsecond molecular dynamic simulations. The dissolution process was also simulated in 1-ethyl-3-methylimidazolium acetate (EmimAc) as an efficient ionic liquid in cellulose dissolution and the results were compared with the aqueous conditions. While the cellulose bunch showed a stable and insoluble structure in pure water, it was completely and efficiently dissolved in both NMMO monohydrate and EmimAc. It was shown that the dissolution time of cellulose in NMMO monohydrate is almost twice that in EmimAc, which is in agreement with the experimental observations. Although it is revealed that hydrogen bonding is the main driving force of cellulose dissolution in NMMO monohydrate, one cannot explain the complete molecular mechanism of NMMO-induced cellulose dissolution only by considering hydrogen bonds. A straightforward molecular mechanism was proposed, in which the interactions of NMMO molecules, not with cellulose, but with the other NMMO molecules play a critical role in the dissolution process.

Electrostatic interactions of enzymes in non-aqueous conditions: insights from molecular dynamics simulations

Electrostatic interactions of enzymes and their effects on enzyme activity and stability are poorly understood in non-aqueous conditions. Here, we investigate the contribution of the electrostatic interactions on the stability and activity of enzymes in the non-aqueous environment using molecular dynamics simulations. Lipase was selected as active and lysozyme as inactive model enzymes in non-aqueous media. Hexane was used as a common non-aqueous solvent model. In agreement with the previous experiments, simulations show that lysozyme has more structural instabilities than lipase in hexane. The number of hydrogen bonds and salt bridges of both enzymes is dramatically increased in hexane. In contrast to the other opinions, we show that the increase of the electrostatic interactions in non-aqueous media is not so favorable for enzymatic function and stability. In this condition, the newly formed hydrogen bonds and salt bridges can partially denature the local structure of the enzymes. For lysozyme, the changes in electrostatic interactions occur in all domains including the active site cleft, which leads to enzyme inactivation and destabilization. Interestingly, most of the changes in electrostatic interactions of lipase occur far from the active site regions. Therefore, the active site entrance regions remain functional in hexane. The results of this study reveal how the changes in electrostatic interactions can affect enzyme stability and activity in non-aqueous conditions. Moreover, we show for the first time how some enzymes, such as lipase, remain active in a non-aqueous environment.Communicated by Ramaswamy H. Sarma.

Enhanced activity of Candida antarctica lipase B in cholinium aminoate ionic liquids: a combined experimental and computational analysis

As a class of ionic liquids with higher biocompatibility, cholinium aminoates ([Cho][AA]) hold potential as solvation media for enzymatic bioprocessing. Herein, solvation effect of [Cho][AA] on structural stability and enzymatic activity of Candida antarctica lipase B (CALB) was evaluated using experimental and computational approaches. Influence of [Cho][AA] on CALB stability was investigated using amino acid anions ([AA]-) with varying hydrophobicity levels. Choline phenylalaninate ([Cho][Phe]) resulted in 109.1% and 110.4% of relative CALB activity to buffer medium at 25 °C and 50 °C, respectively. Simulation results revealed the improvement of CALB's enzymatic activities by [AA]- with a strong hydrophobic character. Shielding of CALB from water molecules by [AA]- was observed. The level of CALB activity was governed by accumulation level of [AA]- at CALB's first hydration layer. The stronger interaction between His224 and Asp187 was postulated to be driven by [Cho][AA], resulting in the activity enhancement of CALB. The slight improvement of CALB activity in 0.05 M [Cho][Phe] at 50 °C could be due to the larger size of entrance to the catalytic site and the stronger interaction between the catalytic residues. The promising effect of [Cho][Phe] on CALB activation may stimulate research efforts in designing a 'fully green' bioreaction for various industrial applications.Communicated by Ramaswamy H. Sarma.

Supercritical CO2/Deep Eutectic Solvent Biphasic System as a New Green and Sustainable Solvent System for Different Applications: Insights from Molecular Dynamics Simulations

Deep eutectic solvents (DESs) are one of the most interesting research subjects in green chemistry nowadays. Due to their low toxicity, simple synthesis, and lower prices, they have gradually taken the place of other green solvents such as ionic liquids (ILs) in sustainable processes. However, problems such as high viscosity and high polarity limit the applications of DESs in areas such as extraction, catalysis, and biocatalysis. In this work, we introduce and evaluate the potential application of scCO2/DES for the first time. Molecular dynamics simulations were used to examine the phase behavior, polarity, molecular mobilities, and microstructure of this system. Results show that CO2 molecules can significantly diffuse to the DES phase, while DES components do not appear in the scCO2 phase. The diffused CO2 molecules significantly enhanced the molecular mobility of the DES components. The presence of CO2 molecules changes the DES polarity so that hexane can be solubilized and dispersed in the DES phase. Radial distribution functions show that the solubilized CO2 molecules have negligible effects on the microstructure of DES. It was shown that chloride and urea are the main interaction sites of CO2 in DES. The results of this study show that scCO2/DES as a new class of green and versatile solvents can open a new promising window for research in sustainable chemistry and engineering.

Flavodoxin in a binary surfactant system consisting of the nonionic 1-decanoyl-rac-glycerol and the zwitterionic lauryldimethylamine-N-oxide: molecular dynamics simulation approach

Due to the short time constant of the spin-spin relaxation process, there is a limitation in the preparation of NMR sample solution for large proteins. To overcome this problem, reverse micelle systems are used.  Here, molecular dynamics simulation was used to study the structure of flavodoxin in a quaternary mixture of 1-decanoyl-rac-glycerol, lauryldimethylamine-N-oxide, pentane and hexanol.  Hexanol was used as co-solvent. Simulations were performed at three different co-solvent concentrations.  The proportion of components in the mixture was selected according to experimental conditions.  For comparison, simulation of flavodoxin in water was also performed.  The simulation results show that the C$$\alpha$$-RMSD for the protein in water is less than for the surfactant mixture.  Also, the radius of gyration of flavodoxin increased in the presence of surfactants.  The distance between the two residues trp-57 and phe-94, as a measure of protein activity, was obtained from the simulations.  The results showed that in the surfactant mixtures this distance increases.  Analysis of the secondary structure of the protein shows that the N-terminal part of the flavodoxin is more affected by surfactants.  The flavodoxin diffusion coefficient in the surfactant mixture decreased in relation to its diffusion coefficient in water.

The effects of mutation and modification on the structure and stability of human lysozyme: A molecular link between carbamylation and atherosclerosis

Amino acid mutations in some proteins such as lysozyme lead to genetically disorder variants and adverse pathogenic consequences. Recently, amino acid modifications were known as a risk factor in many related diseases such as uremia and atherosclerosis, showing the importance of these surface-structure changes. Although the structural consequences of the hereditary proteins have been examined extensively, such effects for the protein modifications are known to a lesser extent. One drawback in the examination of protein modifications is hardness in experimental detection of modifications by techniques such as NMR and crystallography. Molecular modeling and simulation can help to understand such phenomena at the molecular levels. It is more rational that the effects of both mutation and modification can be compared in a single protein model. Here, molecular dynamics simulation is used to compare the effects of a disease-related carbamylation modification and an amyloidogenic mutation (D67H) in human lysozyme as a model protein. The results show that the carbamylation adversely effects on the tertiary structure, leading to the similar unfolding pathway to the hereditary amyloidogenic form. The carbamylation leads to the instability of the overall protein conformation, especially on the β-domain, which is a characteristic of hereditary amyloidosis in human lysozymes. The aggregation behaviors of both modified and mutant lysozyme were examined by molecular docking calculations. The results showed that the partially unfolded lysozyme might form tight protein aggregates upon carbamylation similar to the amyloidogenic variant. Both single and all-residues carbamylations impose serious conformational changes to the tertiary structure of lysozyme. It was obtained that carbamylation of lysozyme strongly effects on the stability of N-terminal β-sheet, which can produce a highly unstable conformation. The results of this study not only show the adverse structural consequences of a disease-associated post-translational modification, but it also may be very helpful to understand the molecular basis for many carbamylation-related diseases such as atherosclerosis in ESRD patients. The results show that non-native post-translational modifications may be as structurally important as hereditary mutations.

Modeling Solvation in Supercritical CO2

In recent decades, a microscopic understanding of solute-solvent intermolecular interactions has been key to advances in technologies based on supercritical carbon dioxide. In many cases, computational work has provided the impetus for new discoveries, shedding new light on important concepts such as the local structure around the solute in the supercritical medium, the influence of the peculiar properties of the latter on the molecular behavior of dissolved substances and, importantly, CO₂ -philicity. In this Review, the theoretical work that has been relevant to these developments is surveyed and, by presenting some crucial open questions, the possible routes to achieving further progress based on the interplay between theory and experiments is discussed.

X-Ray Crystallography as a Tool to Determine Three-Dimensional Structures of Commercial Enzymes Subjected to Treatment in Pressurized Fluids

The study of enzyme function often involves a multi-disciplinary approach. Several techniques are documented in the literature towards determining secondary and tertiary structures of enzymes, and X-ray crystallography is the most explored technique for obtaining three-dimensional structures of proteins. Knowledge of three-dimensional structures is essential to understand reaction mechanisms at the atomic level. Additionally, structures can be used to modulate or improve functional activity of enzymes by the production of small molecules that act as substrates/cofactors or by engineering selected mutants with enhanced biological activity. This paper presentes a short overview on how to streamline sample preparation for crystallographic studies of treated enzymes. We additionally revise recent developments on the effects of pressurized fluid treatment on activity and stability of commercial enzymes. Future directions and perspectives on the the role of crystallography as a tool to access the molecular mechanisms underlying enzymatic activity modulation upon treatment in pressurized fluids are also addressed.

Synthesis of hierarchically structured ZnO nanomaterials via a supercritical assisted solvothermal process

Hierarchically structured ZnO nanomaterials with flower-sheet-particle morphologies were synthesized via a supercritical assisted solvothermal process free from any other auxiliary chemicals.

Biosynthesis of Flavour-Active Esters via Lipase-Mediated Reactions and Mechanisms

Flavour active esters belong to one group of fine aroma chemicals that impart desirable fruity flavour notes and are widely applied in the flavour and fragrance industry. Due to the increasing consumer concern about health, natural products are attracting more attention than chemically synthesized substances. The biosynthesis of flavour-active esters via lipase-catalyzed reactions is one of the most important biotechnological methods for natural flavour generation. To proceed with the industrial production of esters on a large scale, it is critical to understand the enzyme properties and behaviours under different reaction conditions. In this short review, the lipase-catalyzed reactions in various systems and their mechanisms for synthesis of the esters are summarized and discussed.