Visualizing structural changes of egg avidin to thermal and electric field stresses by molecular dynamics simulation

Effects of theacrine on the astringency of EGCG by affecting salivary protein - EGCG interactions through different molecular mechanisms

(-)-Epigallocatechin gallate (EGCG) and theacrine are involved in imparting tea with its astringent and bitter tastes. This study investigated the effect of theacrine on the astringency of EGCG and its molecular mechanism. Sensory evaluation was used to study the astringent intensities of EGCG solutions in the presence and absence of various concentrations of theacrine. The results indicated a considerable increase in the astringency values of EGCG-theacrine solutions compared with those of EGCG solutions alone. Furthermore, dynamic light scattering (DLS) and molecular dynamics simulations (MD) were to explore the interaction mechanisms. The results revealed that theacrine increased the particle size of EGCG-proline-rich proteins (PRPs) aggregates with that of EGCG and PRPs alone. MD revealed that theacrine potentially acted as a bridge between EGCG and PRPs, promoting their interaction and intensifying the EGCG's astringency. However, theacrine could not bridge two or more mucins owing to the substantial spatial structure of mucin.

MD simulation to comprehend polygalacturonase inactivation mechanism during thermal and non-thermal effects of infrared processing

Food quality is greatly impacted by traditional heat methods for polygalacturonase (PG) inactivation; therefore, it's imperative to develop a novel infrared (IR) inactivation approach and identify its mechanism. Utilizing molecular dynamics (MD) simulation, this study verified the PG's activity, structure, active sites, and substrate channel under the single thermal and non-thermal effects of IR. PG activity was significantly reduced by IR, and structure was unfolded by increasing random coils (65.62 %) and decreasing β-sheets (29.11 %). MD data indicated that the relative locations of PG's active sites were altered by both IR effects, and the enzyme-substrate channel was shortened (10.53 % at 18 μm and 15.79 % at 80 °C). The thermal effect of IR on the inactivation of PG was significantly more pronounced than its non-thermal effect. This study unveiled the mechanism by which the infrared disrupted PG's activity, active sites, and substrate channels; thus, it expanded the infrared technique's efficacy in enzyme control.

Molecular dynamics investigation on synthesis of a pH- and temperature-sensitive carbon nanotube loaded with doxorubicin

The many exotic properties of carbon nanotubes (CNTs) make them a powerful attraction in the field of drug delivery systems (DDS). In this work, based on quantum chemical calculation and molecular simulation techniques, polyacrylic acid (PAA) and N-isopropyl acrylamide (NIP) are selected and acted simultaneously on the CNT to form a stable system (FCNT). As a potential DDS, FCNT captures the dispersed doxorubicin (DOX) molecules around it and maintains a stable configuration. In these processes, electrostatic and van der Waals forces act synergistically, with van der Waals forces dominating. Compared to NIP, PAA molecules exhibit stronger adhesion and encapsulation efficiency to CNT and stronger adsorption capacity to DOX. This study reveals the mechanism of action among PAA, NIP, CNT, and DOX, providing feasibility verification and prospective guidance for the experimental synthesis of PAA-NIP-CNT-type multifunctional DDS, and also broadening the idea for exploring more efficient DDS suitable for DOX.

Assessment of cell wall degrading enzymes by molecular docking and dynamics simulations: Effects of novel infrared treatment

Cell wall-degrading enzymes' activities under infrared treatment are vital for peeling; it is critical to elucidate the mechanisms of the novel infrared peeling in relation to its impact on cell wall-degrading enzymes. In this study, the activities, and gene expressions of eight degrading enzymes closely related to pectin, cellulose and hemicellulose were determined. The most influential enzyme was selected from them, and then the mechanism of its changes was revealed by molecular dynamics simulation and molecular docking. The results demonstrated that infrared had the most significant effect on β-glucosidase among the tested enzymes (increased activity and up-regulated gene expression of 195.65 % and 7.08, respectively). It is suggested infrared crucially promotes cell wall degradation by affecting β-glucosidase. After infrared treatment, β-glucosidase's structure moderately transformed to a more open one and became flexible, increasing the affinity between β-glucosidase and substrate (increasing 75 % H-bonds and shortening 15.89 % average length), thereby improving β-glucosidase's activity. It contributed to cell wall degradation. The conclusion is that the effect of infrared on the activity, gene expression and molecular structure of β-glucosidase causes damage to the peel, thus broadening the applicability of the new infrared dry-peeling technique, which has the potential to replace traditional wet-peeling methods.

Effects of temperature and microwave on the stability of the blast effector complex APikL2A/sHMA25 as determined by molecular dynamics analyses

Magnaporthe oryzae is the causal agent of rice blast, and understanding how abiotic stress affects the resistance of plants to this disease is useful for designing disease control strategies. In this paper, the effects of temperature and microwave irradiation on the effector complex comprising APikL2A from M. oryzae and sHMA25 from foxtail millet were investigated by molecular dynamics simulations using the GROMACS software package. While the structure of APikL2A/sHMA25 remained relatively stable in a temperature range of 290 K (16.85 °C) to 320 K (46.85 °C), the concave shape of the temperature-dependent binding free energy curve indicated that there was maximum binding affinity between APikL2A and sHMA25 at 300 K-310 K. This coincided with the optimum infectivity temperature, thus suggesting that coupling of the two polypeptides may play a role in the infection process. A strong oscillating electric field destroyed the structure of APikL2A/sHMA25, although it was stable and not susceptible to weak electric fields.

Prediction and validation of monoclonal antibodies separation in aqueous two-phase system using molecular dynamic simulation

In order to predict how mAbs partition in 20% ethylene oxide/80% propylene oxide (v/v) random copolymer (EO₂₀PO₈₀)/water aqueous two-phase system (ATPS), a molecular dynamic simulation model was developed using Gromacs and then validated by experiments. The ATPS was applied with seven kinds of salt, including buffer salt and strong dissociation salt that were commonly employed in the purification of protein. Na₂SO₄ was shown to have the best effects on lowering EO₂₀PO₈₀ content in the aqueous phase and enhancing recovery. The content of EO₂₀PO₈₀ in the sample solution was decreased to 0.62%±0.25% and the recovery of rituximab increased to 97.88%±0.95% by adding 300 mM Na₂SO₄ into back extraction ATPS. The viability determined by ELISA was 95.57% at the same time. A strategy for constructing a prediction model for the distribution of mAbs in ATPS was proposed in consideration of this finding. Partition of trastuzumab in ATPS was predicted by the model created using this method and the prediction result was further validated by experiments. The recovery of trastuzumab reached 95.63%±2.86% under the ideal extraction conditions suggested by the prediction model.

Understanding the Mechanism of Increased IgG/IgE Reactivity but Decreased Immunodetection Recovery in Thermally Induced Shrimp (Litopenaeus vannamei) Tropomyosin via Multispectroscopic and Molecular Dynamics Simulation Techniques

Despite the fact that tropomyosin (TM) has highly stable structural characteristics, thermal processing can adversely influence its immunodetection, and the mechanism involved has not been elucidated. Purified TM was heated at various temperatures, and then the IgG/IgE-binding capacity and immunodetection recovery were determined; meanwhile, the structural alterations were analyzed via spectroscopic and molecular dynamics simulation techniques. The obtained results demonstrated that heat-treated TM showed significantly increased IgG/IgE reactivity, confirmed by indirect ELISA and immunoblotting analysis, which might be attributed to the increased structural flexibility, and thus allowed TM to be recognized IgG/IgE easily. However, these structural alterations during thermal processing would contribute to the masking of some epitopes located in TM's surface due to the presence of curled or folded conformation with a considerable reduction of the solvent-accessible surface and radius of gyration, which primarily caused immunodetection recovery reduction in the sandwich ELISA (sELISA) test. The number of antigen binding sites might play a crucial role in a sandwich immunodetection system for sensitive and precise analysis in processed foods.

Effect of Structural Targeted Modifications on the Potential Allergenicity of Peanut Allergen Ara h 2

Protein structure affects allergenicity, and critical structural elements, especially conformational epitopes that determine allergenicity, have attracted a great deal of interest. In this study, we aimed to identify the localized structure that affects the potential allergenicity of protein by making targeted modifications of Ara h 2 and comparing the structure and allergenicity of mutants with those of the wide-type allergen. The structures of the allergen and its mutants were characterized by circular dichroism and ultraviolet absorption spectroscopy and simulated by molecular dynamics. The allergenicity was assessed by Western blotting, an indirect competitive enzyme-linked immunosorbent assay, a cell model, and a mouse model. Then, the structures that affect allergenicity were analyzed and screened. Our results showed that mutations in amino acids changed the nearby localized structure and the overall structures. The structural changes affected the IgE binding capacity of the allergen and reduced its potential allergenicity. The solvent accessible surface area (SASA) of aromatic residues was positively correlated with the IgE binding capacity. The integrity of the disulfide bond is also critical for the binding of IgE to allergens. Interestingly, different mutations induced similar electrostatic potential and allergenicity changes, such as localized structure R⁶²DPYSPSQDPYSPS⁷⁵. In conclusion, the disulfide bond and the SASA of aromatic residues are important for the allergenicity of Ara h 2. The localized structure R⁶²DPYSPSQDPYSPS⁷⁵ is also crucial for the allergenicity of Ara h 2.

Molecular Dynamics Research of Spatial Orientation and Kinetic Energy of Active Site Collision of Carnosine under Weak Microwave Irradiation

The molecular mechanism of the microwave nonthermal effect is still not clear. This work investigated the spatial orientation and kinetic energy of active site collision of carnosine, a natural bioactive dipeptide, under the weak microwave irradiation using the molecular dynamics simulation. Our results showed the influences of the temperature, microwave intensity, microwave frequency, and microwave polarization mode (linear polarization and circular polarization) on the spatial orientation and kinetic energy of active site collision of carnosine. First, under the constant intensity and frequency of linear polarization microwave irradiation, the increment of the collision probability between the 6N atom of carnosine and the 28H atom of the other carnosine at effective space angle decreases from 85.0% to 3.5% with increasing temperature. Second, with the increase of microwave intensity, the change of spatial orientation and kinetic energy becomes more and more significant. However, the change of circular polarization microwaves on the spatial orientation and kinetic energy of collision is weaker than that of linear polarization. Third, under the constant intensity of linear polarization microwave irradiation, the collision probability between the 6N atom and the 28H atom at effective space angle decreases from 70.2% to 14.7% with increasing frequency. Finally, under the microwave polarization, the spatial orientation and kinetic energy of molecular collision are changed, which is summarized as the microwave postpolarization effect (MWPPE). The dependence of MWPPE on temperature, microwave intensity, microwave frequency, and polarization mode is very complicated. In the end, this effect can provide a new insight into the molecular mechanism of the microwave nonthermal effect.

Mechanism of trypsin activation by pulsed electric field treatment revealed based on chemical experiments and molecular dynamics simulations

A pulsed electric field (PEF) treatment exhibits different effects on trypsin; however, the mechanism of enzyme activation remains unclear. Herein, chemical experiments combined with molecular dynamics simulations revealed the mechanism of trypsin activation by PEF treatment at the molecular level. The results indicated that compared with the values at 0 kV/cm, the enzyme activity, Vmax, and Kcat at 20 kV/cm increased by 9.30%, 4.74%, and 4.30%, respectively, and Km decreased by 11.14%, indicating an improved interaction between the enzyme and substrate. The simulation results revealed that PEF treatment increased the number of molecular hydrogen bonds and the solvent-accessible surface area, while decreasing the rotation radius and random coil content by 5.00% and 3.37%, respectively. Molecular docking indicated that PEF treatment altered the active center and increased the affinity between the enzyme and substrate. The simulation results were consistent with those of the spectroscopic experiments conducted on trypsin after PEF treatment.

An Overview of Molecular Dynamics Simulation for Food Products and Processes

Molecular dynamics (MD) simulation is a particularly useful technique in food processing. Normally, food processing techniques can be optimized to favor the creation of higher-quality, safer, more functional, and more nutritionally valuable food products. Modeling food processes through the application of MD simulations, namely, the Groningen Machine for Chemical Simulations (GROMACS) software package, is helpful in achieving a better understanding of the structural changes occurring at the molecular level to the biomolecules present in food products during processing. MD simulations can be applied to define the optimal processing conditions required for a given food product to achieve a desired function or state. This review presents the development history of MD simulations, provides an in-depth explanation of the concept and mechanisms employed through the running of a GROMACS simulation, and outlines certain recent applications of GROMACS MD simulations in the food industry for the modeling of proteins in food products, including peanuts, hazelnuts, cow’s milk, soybeans, egg whites, PSE chicken breast, and kiwifruit.