Molecular dynamics simulation for mechanism revelation of the safety and nutrition of lipids and derivatives in food: State of the art

Investigation of self-assembly mechanism of gluten protein amyloid fibrils and molecular characterization of structure units

The mechanism of peptides self-assembly into gluten amyloid fibrils was explored through bond-breaking experiments and molecular dynamics (MD) simulations, verified through fibrillation experiments using synthetic peptides. The disruption of hydrogen bonds reduced thioflavin T fluorescence intensity and average particle size of gluten amyloid fibrils by 24 % and 81 %, respectively, causing a breakdown of internal structure. Disruption of electrostatic and hydrophobic forces induced further aggregation of fibrils. MD simulation revealed that peptides transitioned from a dispersed state to aggregation, followed by changes in secondary structure, culminating in the formation of stacked β-sheets structure units. Hydrogen bonding emerged as the primary driver of self-assembly with contributions from hydrophobic and electrostatic interactions. The synthetic single or hybrid peptide systems selected by MD formed ribbon- or fiber-like amyloid fibrils with inter-strand distance of 4.7 Å and respective inter-sheet distances of 10.2 Å and 10.8 Å, suggesting that the structure and morphology of eventual amyloid fibrils were affected by the peptide sequence and cross β-sheet structure units.

Highly cost-effective wheat starch-stearic acid complexes enabled by microwave processing: Structural properties, anti-digestion, and molecular dynamics simulation

Microwave (MW) heating shows higher efficiency in preparing wheat starch-stearic acid (WS-SA) complexes than the traditional water bath (WB) heating method, while the detailed "time-energy-quality" evaluations and the potential anti-digestion mechanism of the MW-processed WS-SA remain further exploration. In this study, 95 % time cost and 73 % energy consumption were saved when using MW processing WS-SA, and the MW-processed complexes were verified to show significantly higher relative crystallinity, short-range ordered structure degree, thermal stability, complex index, and resistant starch content. Molecular dynamics (MD) simulation demonstrated that MW treatment notably facilitated the binding rate of amylose and SA molecules, generating a tight and stable helical structure through hydrogen bonds and van der Waals forces. Analyses of solvent-accessible surface area and water status cross-verified that the denser structure could endow the MW-processed complexes with higher resistance to water solvation effects and correspondingly reduce the water mobility for enzymatic hydrolysis reactions, ultimately making the MW-processed complexes more undigestible. This study provides a further understanding of the anti-digestion mechanisms of the MW-processed WS-SA from the molecular level, and it is expected that the current work could attract more concerns to the highly cost-effective MW heating method for processing starchy food.

Supramolecular assembly strategy of modified starch chains for achieving recyclable emulsion biocatalysis within a narrow pH range

Stimuli-responsive Pickering emulsions are promising in biocatalysis for their ease of product separation and emulsifier recovery. However, pH responsiveness, though simple and cost-effective, faces challenges in precise control and narrow transition ranges, limiting its use in enzymatic catalysis. Herein we introduced amorphous octenyl succinic anhydride-modified debranched starch chains (Am-OSA-St) to control emulsion properties within a pH range suitable for enzymatic catalysis. By adjusting the OSA group density and molecular weight, Am-OSA-St allowed emulsions to transition reversibly between pH 7.3 and 5.5 and enabled self-recycling through supramolecular self-assembly. Employing molecular dynamics simulations and physicochemical characterization, we elucidated the control mechanism of oil-water interfaces via the microstructure transformation of Am-OSA-St. The findings revealed that protonation of carboxylate groups disrupted the charge balance and polarity of starch chains, leading to strong electrostatic and van der Waals interactions that drove self-assembly. This entanglement caused starch chains in the aqueous phase to "drag" those at the oil-water interface, moving them into the aqueous phase and forming micelles. These micelles, with a hydrophobic interior and hydrophilic exterior, prevented re-adsorption. Testing with Candida antarctica Lipase B (CALB) and N-acetylneuraminic lyase showed that the pH-regulated emulsion system maintained excellent efficiency and cycling stability in mild conditions.

Application of molecular dynamics simulation in the field of food enzymes: improving the thermal-stability and catalytic ability

Enzymes can produce high-quality food with low pollution, high function, high acceptability, and medical aid. However, most enzymes, in their native form, do not meet the industrial requirements. Sequence-based and structure-based methods are the two main strategies used for enzyme modification. Molecular Dynamics (MD) simulation is a sufficiently comprehensive technology, from a molecular perspective, which has been widely used for structure information analysis and enzyme modification. In this review, we summarize the progress and development of MD simulation, particularly for software, force fields, and a standard procedure. Subsequently, we review the application of MD simulation in various food enzymes for thermostability and catalytic improvement was reviewed in depth. Finally, the limitations and prospects of MD simulation in food enzyme modification research are discussed. This review highlights the significance of MD simulation and its prospects in food enzyme modification.

Recent advances in computational prediction of molecular properties in food chemistry

The combination of food chemistry and computational simulation has brought many impacts to food research, moving from experimental chemistry to computer chemistry. This paper will systematically review in detail the important role played by computational simulations in the development of the molecular structure of food, mainly from the atomic, molecular, and multicomponent dimension. It will also discuss how different computational chemistry models can be constructed and analyzed to obtain reliable conclusions. From the calculation principle to case analysis, this paper focuses on the selection and application of quantum mechanics, molecular mechanics and coarse-grained molecular dynamics in food chemistry research. Finally, experiments and computations of food chemistry are compared and summarized to obtain the best balance between them. The above review and outlook will provide an important reference for the intersection of food chemistry and computational chemistry, and is expected to provide innovative thinking for structural research in food chemistry.

Application of the molecular dynamics simulation GROMACS in food science

Food comprises proteins, lipids, sugars and various other molecules that constitute a multicomponent biological system. It is challenging to investigate microscopic changes in food systems solely by performing conventional experiments. Molecular dynamics (MD) simulation serves as a crucial bridge in addressing this research gap. The Groningen Machine for Chemical Simulations (GROMACS) is an open-source, high-performing molecular dynamics simulation software that plays a significant role in food science research owing to its high flexibility and powerful functionality; it has been used to explore the molecular conformations and the mechanisms of interaction between food molecules at the microcosmic level and to analyze their properties and functions. This review presents the workflow of the GROMACS software and emphasizes the recent developments and achievements in its applications in food science research, thus providing important theoretical guidance and technical support for obtaining an in-depth understanding of the properties and functions of food.

Molecular simulation for food protein-ligand interactions: A comprehensive review on principles, current applications, and emerging trends

In recent years, investigations on molecular interaction mechanisms between food proteins and ligands have attracted much interest. The interaction mechanisms can supply much useful information for many fields in the food industry, including nutrient delivery, food processing, auxiliary detection, and others. Molecular simulation has offered extraordinary insights into the interaction mechanisms. It can reflect binding conformation, interaction forces, binding affinity, key residues, and other information that physicochemical experiments cannot reveal in a fast and detailed manner. The simulation results have proven to be consistent with the results of physicochemical experiments. Molecular simulation holds great potential for future applications in the field of food protein-ligand interactions. This review elaborates on the principles of molecular docking and molecular dynamics simulation. Besides, their applications in food protein-ligand interactions are summarized. Furthermore, challenges, perspectives, and trends in molecular simulation of food protein-ligand interactions are proposed. Based on the results of molecular simulation, the mechanisms of interfacial behavior, enzyme-substrate binding, and structural changes during food processing can be reflected, and strategies for hazardous substance detection and food flavor adjustment can be generated. Moreover, molecular simulation can accelerate food development and reduce animal experiments. However, there are still several challenges to applying molecular simulation to food protein-ligand interaction research. The future trends will be a combination of international cooperation and data sharing, quantum mechanics/molecular mechanics, advanced computational techniques, and machine learning, which contribute to promoting food protein-ligand interaction simulation. Overall, the use of molecular simulation to study food protein-ligand interactions has a promising prospect.

Molecular dynamics simulation of the interaction between palmitic acid and high pressure CO2

In this study, molecular dynamics simulation was used to explore the interaction characteristics of palmitic acid and CO2, and the effects of temperature and pressure on the solubility of palmitic acid in CO2 were investigated. In the range of 293-353 K and 5-30 MPa, the snapshot of palmitic acid distribution in CO2 shows that the molecular chain of palmitic acid in high-density CO2 system is more straight and more dispersed than that in low-density CO2 system. The radial distribution function further clearly shows that the solubility of palmitic acid in CO2 decreases with the increase of temperature and increases with the increase of pressure, which is consistent with the fatty acid solubility data reported in the literature and the setting rules of supercritical CO2 extraction process conditions. As the temperature decreases and the pressure increases, the interaction energy between palmitic acid and CO2 increases, which is conducive to overcoming the intermolecular force of palmitic acid and promoting dissolution. The solubility parameters of palmitic acid and CO2 can better reflect the trend of palmitic acid solubility changing with temperature and pressure, which can play a guiding role in the determination of process conditions and even the development of new processes.

Assembly of Helical Nanostructures: Solvent-Induced Morphology Transition and Its Effect on Cell Adhesion

Being able to precisely manipulate both the morphology and chiroptical signals of supramolecular assemblies will help to better understand the natural biological self-assembly mechanism. Two simple l/d-phenylalanine-based derivatives (L/DPFM) have been designed, and their solvent-dependent morphology evolutions are illustrated. It was found that, as the content of H₂ O in aqueous ethanol solutions was increased, LPFM self-assembles first into right-handed nanofibers, then flat fibrous structures, and finally inversed left-handed nanofibers. Assemblies in ethanol and H₂ O exhibit opposite conformations and circular dichroism (CD) signals even though they are constructed from the same molecules. Thus, the morphology-dependent cell adhesion and proliferation behaviors are further characterized. Left-handed nanofibers are found to be more favorable for cell adhesion than right-handed nanostructures. Quantitative AFM analysis showed that the L929 cell adhesion force on left-handed LPFM fibers is much higher than that on structures with inversed handedness. Moreover, the value of cell Young's modulus is lower for left-handed nanofibrous films, which indicates better flexibility. The difference in cell-substrate interactions might lead to different effects on cell behavior.

Enhancing the Inhibition Potential of AHL Acylase PF2571 against Food Spoilage by Remodeling Its Substrate Scope via a Computationally Driven Protein Design

The N-acyl homoserine lactone (AHL) acylases are widely used as quorum sensing (QS) blockers to inhibit bacterial food spoilage. However, their substrate specificity for long-chain substrates weakens their efficiency. In this study, a computer-assisted design of AHL acylase PF2571 was performed to modify its substrate scope. The results showed that the variant PF2571^{H194Y, L221R} could effectively quench N-hexanoyl-l-homoserine lactone and N-octanoyl-l-homoserine lactone without impairing its activity against long-chain AHLs. Kinetic analysis of the enzymatic activities further corroborated the observed substrate expansion. The inhibitory activities of this variant were significantly enhanced against the QS phenotype of Aeromonas veronii BY-8, with inhibition rates of 45.67, 78.25, 54.21, and 54.65% against proteases, motility, biofilms, and extracellular polysaccharides, respectively. Results for molecular dynamics simulation showed that the steric hindrance, induced by residue substitution, could have been responsible for the change in substrate scope. This study dramatically improves the practicability of AHL acylase in controlling food spoilage.