Molecular Dynamics Simulation for Mechanism Elucidation of Food Processing and Safety: State of the Art

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.

Flavor Perception and Formation Mechanism of Empty Cup Aroma in Soy Sauce Aroma Type Baijiu

The research focused on the distinctive empty cup aroma, with the aim of identifying the key aroma compounds and the formation mechanism of empty cup aroma in soy sauce aroma type baijiu (SSB). The lasting times of SSB is significantly longer than that of other types of baijiu, with an average duration of 28 days. Key compounds such as 2,3-dimethyl-5-ethylpyrazine, phenylethyl alcohol, p-cresol, sotolon, benzeneacetic acid were identified in empty cup aroma due to their highest flavor dilution factor. Molecular dynamics (MD) simulation was performed to study the mechanism of empty cup aroma on the liquid-gas interface and solid-gas interface. The results revealed the existence of hydrogen bonding and van der Waals forces between sotolon and lactic acid, a representative nonvolatile compound, which are speculated to be an important reason for the empty cup aroma.

Inclusion complexes of β-cyclodextrin with isomeric ester aroma compounds: Preparation, characterization, mechanism study, and controlled release

Cyclodextrins (CDs) have been discovered to provide an efficient solution to the limited application of ester aroma molecules used in food, tobacco, and medication due to their strong smell and unstable storage. This work combined molecular modeling and experimental to analyze the conformation and controlled release of isomeric ester aroma compounds/β-CD inclusion complexes (ICs). The investigation revealed that ester aroma compounds could be effectively encapsulated within the β-CD cavity, forming ICs with low binding affinity. Furthermore, the key driving forces in ICs were identified as hydrogen bonds and van der Waals interactions through theoretical simulation. Results from the Fourier transform infrared (FTIR), nuclear magnetic resonance (NMR) and Isothermal titration calorimetry (ITC) experiments confirmed the intermolecular interaction predicted by the molecular model. Notably, the release rate of aroma compounds from L-menthyl acetate/β-CD (LMA/β-CD) IC exceeded that of terpinyl acetate/β-CD (TA/β-CD) IC. This difference is attributed to the length of the chain of aroma molecules and the variation in the position of functional groups, influencing the stable formation of ICs with β-CD. These findings hold potential implications for refining the application of ICs across diverse industries.

Glycans modulate lipid binding in Lili-Mip lipocalin protein: insights from molecular simulations and protein network analyses

The unique viviparous Pacific Beetle cockroaches provide nutrition to their embryo by secreting milk proteins Lili-Mip, a lipid-binding glycoprotein that crystallises in-vivo. The resolved in-vivo crystal structure of variably glycosylated Lili-Mip shows a classical Lipocalin fold with an eight-stranded antiparallel beta-barrel enclosing a fatty acid. The availability of physiologically unaltered glycoprotein structure makes Lili-Mip a very attractive model system to investigate the role of glycans on protein structure, dynamics, and function. Towards that end, we have employed all-atom molecular dynamics simulations on various glycosylated stages of a bound and free Lili-Mip protein and characterised the impact of glycans and the bound lipid on the dynamics of this glycoconjugate. Our work provides important molecular-level mechanistic insights into the role of glycans in the nutrient storage function of the Lili-Mip protein. Our analyses show that the glycans stabilise spatially proximal residues and regulate the low amplitude opening motions of the residues at the entrance of the binding pocket. Glycans also preserve the native orientation and conformational flexibility of the ligand. However, we find that either deglycosylation or glycosylation with high-mannose and paucimannose on the core glycans, which better mimic the natural insect glycosylation state, significantly affects the conformation and dynamics. A simple but effective distance- and correlation-based network analysis of the protein also reveals the key residues regulating the barrel's architecture and ligand binding characteristics in response to glycosylation.

Structure-directed bioengineering the lid1 of cold-adapted Pseudomonas sp. TB11 esterase to boost catalytic capacity

Structure-guided bioengineering enzymes has been an efficient strategy to obtain biocatalyst with desirable properties. In this study, the cold-adapted esterase from Pseudomonas sp. (CPE) was optimized through bioinformatic-based structured-guided bioengineering on lid1 region. Substitutions of non-conserved Q55 led to noticeable increase in hydrolysis without sacrificing enzyme thermostability, activating effects of Ca2+ and organic solvents. Compared to the wild type, both of Q55V and Q55N among the constructed variants exhibited about a 2.0-fold and 6.5-fold higher hydrolytic activity toward short-chain and long-chain substrates, respectively. In contrast, lid swapping with the lid of Thermomyces lanuginosus lipase reduced the activity and thermostability of CPE. Catalytic kinetics revealed that substitution of Q55 with Y, V, N and R enhanced the substrate affinity of CPE. Hydrolysis by Q55V remarkedly enriched the characteristic flavor components of single cream. The study sheds light on structure-guided bioengineering of lid tailoring cold-adapted esterases with desired catalytic performance to meet the demand from biotechnological applications.

Unraveling the Phase Behavior, Mechanical Stability, and Protein Reconstitution Properties of Polymer-Lipid Hybrid Vesicles

Hybrid vesicles consisting of natural phospholipids and synthetic amphiphilic copolymers have shown remarkable material properties and potential for biotechnology, combining the robustness of polymers with the biocompatibility of phospholipid membranes. To predict and optimize the mixing behavior of lipids and copolymers, as well as understand the interaction between the hybrid membrane and macromolecules like membrane proteins, a comprehensive understanding at the molecular level is essential. This can be achieved by a combination of molecular dynamics simulations and experiments. Here, simulations of POPC and PBD22-b-PEO14 hybrid membranes are shown, uncovering different copolymer configurations depending on the polymer-to-lipid ratio. High polymer concentrations created thicker membranes with an extended polymer conformation, while high lipid content led to the collapse of the polymer chain. High concentrations of polymer were further correlated with a decreased area compression modulus and altered lateral pressure profiles, hypothesized to result in the experimentally observed improvement in membrane protein reconstitution and resistance toward destabilization by detergents. Finally, simulations of a WALP peptide embedded in the bilayer showed that only membranes with up to 50% polymer content favored a transmembrane configuration. These simulations correlate with previous and new experimental results and provide a deeper understanding of the properties of lipid-copolymer hybrid membranes.

More simple, efficient and accurate food research promoted by intermolecular interaction approaches: A review

The investigation of intermolecular interactions has become increasingly important in many studies, mainly by combining different analytical approaches to reveal the molecular mechanisms behind specific experimental phenomena. From spectroscopic analysis to sophisticated molecular simulation techniques like molecular docking, molecular dynamics (MD) simulation, and quantum chemical calculations (QCC), the mechanisms of intermolecular interactions are gradually being characterized more clearly and accurately, leading to revolutionary advances. This article aims to review the progression in the main techniques involving intermolecular interactions in food research and the corresponding experimental results. Finally, we discuss the significant impact that cutting-edge molecular simulation technologies may have on the future of conducting deeper exploration. Applications of molecular simulation technology may revolutionize the food research, making it possible to design new future foods with precise nutrition and desired properties.

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.

Multiscale structure and precipitation mechanism of debranched starch precipitated by different alcohols

Alcohol solution is a cheap, simple, and effective precipitating solvent frequently used for separating debranched starch (DBS), yet little is known about the precipitation mechanism of DBS by different alcohols. This study precipitated DBS from pullulanase-hydrolyzed starch using ethanol, n-butanol, and isopentanol. The multiscale structures of DBS were characterized, including chain length, single/double helix, and crystalline. The chain conformation and precipitation mechanism of DBS in different alcohols was investigated using molecular dynamics (MD) simulation. DBS precipitated by n-butanol contained the largest proportion of short chain (DP6-24, 83.2 %), the highest V-type crystallinity (21.1 %), and the largest single-helix content (24.7 %). A single helix conformation of DBS chain was determined in alcohols, where alcohol molecules entered the helix cavity. Intra/inter-molecular hydrogen bonds stabilized the helix, with a large number of hydrogen bonds leading to strong molecular interaction and stable helical structure. The solvent accessible surface area of DBS chain decreased by 7.88-19.32 % in alcohols, and the radial distribution function revealed that the first solvent layer of DBS chain at 0.29 nm was closely related to hydrogen bonding. This study provides a basis for the choice of precipitation solvent for preparing DBS with different chain lengths and physicochemical properties.

Advances in pulsed electric stimuli as a physical method for treating liquid foods

There is a need for alternative technologies that can deliver safe and nutritious foods at lower costs as compared to conventional processes. Pulsed electric field (PEF) technology has been utilised for a plethora of different applications in the life and physical sciences, such as gene/drug delivery in medicine and extraction of bioactive compounds in food science and technology. PEF technology for treating liquid foods involves engineering principles to develop the equipment, and quantitative biochemistry and microbiology techniques to validate the process. There are numerous challenges to address for its application in liquid foods such as the 5-log pathogen reduction target in food safety, maintaining the food quality, and scale up of this physical approach for industrial integration. Here, we present the engineering principles associated with pulsed electric fields, related inactivation models of microorganisms, electroporation and electropermeabilization theory, to increase the quality and safety of liquid foods; including water, milk, beer, wine, fruit juices, cider, and liquid eggs. Ultimately, we discuss the outlook of the field and emphasise research gaps.

Investigation of the Structure and Allergic Potential of Whey Protein by Both Heating Sterilization and Simulation with Molecular Dynamics

As the main allergens in milk, whey proteins are heat-sensitive proteins and are widespread in dairy products and items in which milk proteins are involved as food additives. The present work sought to investigate the effect of heating sterilization on the allergenicity of α-lactalbumin (α-LA) and β-lactoglobulin (β-LG), the main composite and allergen in whey protein isolate (WPI), by combining molecular dynamics with experimental techniques for detecting the spatial structure and IgE binding capacity. The structure of WPI was basically destroyed at heat sterilization conditions of 95 °C for 5 min and 65 °C for 30 min by SDS-PAGE analysis and spectroscopic analysis. In addition, α-lactalbumin (α-LA) may be more sensitive to temperature, resulting in exposure to allergic epitopes and increasing the allergic potential, while the binding capacity of β-lactoglobulin (β-LG) to IgE was reduced under 65 °C for 30 min. By the radius of gyration (Rg) and root-mean-square deviation (RMSD) plots calculated in molecular dynamics simulations, α-LA was less structurally stable at 368 K, while β-LG remained stable at higher temperatures, indicating that α-LA was more thermally sensitive. In addition, we observed that the regions significantly affected by temperatures were associated with the capacity of allergic epitopes (α-LA 80-101 and β-LG 82-93, 105-121) to bind IgE through root-mean-standard fluctuation (RMSF) plots, which may influence the two major allergens. We inferred that these regions are susceptible to structural changes after sterilization, thus affecting the allergenicity of allergens.

The potential of antifungal peptide Sesquin as natural food preservative

Sesquin is a wide spectrum antimicrobial peptide displaying a remarkable activity on fungi. Contrarily to most antimicrobial peptides, it presents an overall negative charge. In the present study, we elucidate the molecular basis of its mode of action towards biomimetic membranes by NMR and MD experiments. While a specific recognition of phosphatidylethanolamine (PE) might explain its activity in a variety of different organisms (including bacteria), a further interaction with ergosterol accounts for its strong antifungal activity. NMR data reveal a charge gradient along its amide protons allowing the peptide to reach the membrane phosphate groups despite its negative charge. Subsequently, the peptide gets structured inside the bilayer, reducing its order. MD simulations predict that its activity is retained in conditions commonly used for food preservation: low temperatures, high pressure, or the presence of electric field pulses, making Sesquin a good candidate as food preservative.

Whether the Research on Ethanol-Water Microstructure in Traditional Baijiu Should Be Strengthened?

Baijiu is a unique and traditional distilled liquor in China. Flavor plays a crucial rule in baijiu. Up to now, the research on the flavor of baijiu has progressed from the identification of volatile compounds to the research on key aroma compounds, but the release mechanism of these characteristic compounds is still unclear. Meanwhile, volatile compounds account for only a tiny fraction, whereas ethanol and water account for more than 98% of the content in baijiu. By summarizing the ethanol-water hydrogen bond structure in different alcoholic beverages, it was found that flavor compounds can affect the association strength of the ethanol-water hydrogen bond, and ethanol-water can also affect the interface distribution of flavor compounds. Therefore, the research on ethanol-water microstructure in baijiu is helpful to realize the simple visualization of adulteration detection, aging determination and flavor release mechanism analysis of baijiu, and further uncover the mystery of baijiu.

Computer-aided food engineering

Computer-aided food engineering (CAFE) can reduce resource use in product, process and equipment development, improve time-to-market performance, and drive high-level innovation in food safety and quality. Yet, CAFE is challenged by the complexity and variability of food composition and structure, by the transformations food undergoes during processing and the limited availability of comprehensive mechanistic frameworks describing those transformations. Here we introduce frameworks to model food processes and predict physiochemical properties that will accelerate CAFE. We review how investments in open access, such as code sharing, and capacity-building through specialized courses could facilitate the use of CAFE in the transformation already underway in digital food systems.

Molecular dynamics simulation study of covalently bound hybrid coagulants (CBHyC): Molecular structure and coagulation mechanisms

Covalently-bound organic silicate-aluminum hybrid coagulants (CBHyC) have been shown to efficiently remove low molecular weight organic contaminants from wastewater. However, the interaction dynamics and motivations during the coagulation of contaminant molecules by CBHyC are limited. In this study, a molecular dynamics (MD) simulation showed that CBHyC forms core-shell structure with the aliphatic carbon chains gather inside as a core and the hydrophilic quaternary ammonium-Si-Al complexes disperse outside as a shell. This wrapped structure allowed the coagulant to diffuse into solutions easily and capture target contaminants. The adsorption of anionic organic contaminants (e.g., diclofenac) onto the CBHyC aggregates was driven equally by van der Waals forces and electrostatic interactions. Cationic organic contaminants (e.g., tetracycline) were seldom bound to CBHyC because of substantial repulsive forces between cationic molecules and CBHyC. Neutrally-charged organic molecules were generally bound through hydrophobic interactions. For adenine and thymine deoxynucleotide, representatives of antibiotic resistance genes, van der Waals forces and electrostatic interaction became the dominant driving force with further movement for adenine and thymine, respectively. Driving forces between target contaminant and coagulant directly affect the size and stability of formed aggregate, following the coagulation efficiency of wastewater treatment. The findings of this study enrich the database of aggregation behavior between low molecular weight contaminants and CBHyC and contribute to further and efficient application of CBHyC in wastewater treatment.

Mechanisms Underlying the Formation of Amylose- Lauric Acid-β-Lactoglobulin Complexes: Experimental and Molecular Dynamics Studies

The aim of the present study was to reveal the mechanisms underlying the formation of ternary complexes with a model system of amylose (AM), lauric acid (LA), and β-lactoglobulin (βLG) using experimental studies and molecular dynamics (MD) simulations. Experimental analyses showed that hydrophobic interactions and hydrogen bonds contributed more than electrostatic forces to the formation of the AM-LA-βLG complex. MD simulations indicated that interactions between AM and βLG through electrostatic forces and hydrogen bonds, and to a less extent van der Waals forces, and interactions between AM and LA through van der Waals forces, were mostly responsible for complex formation. The combination of experimental results and MD simulations has provided new mechanistic insights and led us to conclude that hydrophobic interactions, van der Waals forces between AM and LA, and van der Waals forces and hydrogen bonds between AM and βLG were the main driving forces for the formation of the AM-LA-βLG complex.

Effects of High Pressure Processing and Thermal Treatment on the Interaction between α-Lactalbumin and Pelargonium-3-Glucoside

In this study, high pressure processing (HPP) and thermal treatment were comparatively evaluated by examining their impacts on the binding behavior and interaction between α-lactalbumin (α-La) and pelargonium-3-glucoside (P3G) under pH values of 6.0, 7.4, and 8.0. The methods of circular dichroism spectroscopy, fluorescence quenching, dynamic light scattering, and molecular simulation were used to characterize the effects of processing-induced changes in protein structure, size distribution, binding site conformation, and residue charges on their binding characteristics between them. The results indicated that the thermal treatments significantly increased the quenching constants of the complex at pH 7.4/8.0 and 60/80 °C, as well as the accessible fraction of protein at pH 8.0/80 °C. Both HPP and thermal treatments increased the random coil content and showed limited effects on the α-helix and β-sheet contents of α-La and caused the aggregation of the complex to varying degrees. Molecular dynamic simulation and docking analyses revealed that the binding site of the complex did not change under different processing conditions, but the solvent-accessible surface area varied under different conditions.

Molecular modeling of lactoferrin for food and nutraceutical applications: insights from in silico techniques

Lactoferrin is a protein, primarily found in milk that has attracted the interest of the food industries due to its health properties. Nevertheless, the instability of lactoferrin has limited its commercial application. Recent studies have focused on encapsulation to enhance the stability of lactoferrin. However, the molecular insights underlying the changes of structural properties of lactoferrin and the interaction with protectants remain poorly understood. Computational approaches have proven useful in understanding the structural properties of molecules and the key binding with other constituents. In this review, comprehensive information on the structure and function of lactoferrin and the binding with various molecules for food purposes are reviewed, with a special emphasis on the use of molecular dynamics simulations. The results demonstrate the application of modeling and simulations to determine key residues of lactoferrin responsible for its stability and interactions with other biomolecular components under various conditions, which are also associated with its functional benefits. These have also been extended into the potential creation of enhanced lactoferrin for commercial purposes. This review provides valuable strategies in designing novel nutraceuticals for food science practitioners and those who have interests in acquiring familiarity with the application of computational modeling for food and health purposes.

Rebuilding the lid region from conformational and dynamic features to engineering applications of lipase in foods: Current status and future prospects

The applications of lipases in esterification, amidation, and transesterification have broadened their potential in the production of fine compounds with high cumulative values. Mostly, the catalytic triad of lipases is covered by either one or two mobile peptides called the "lid" that control the substrate channel to the catalytic center. The lid holds unique conformational allostery via interfacial activation to regulate the dynamics and catalytic functions of lipases, thereby highlighting its importance in redesigning these enzymes for industrial applications. The structural characteristic of lipase, the dynamics of lids, and the roles of lid in lipase catalysis were summarized, providing opportunities for rebuilding lid region by biotechniques (e.g., metagenomic technology and protein engineering) and enzyme immobilization. The review focused on the advantages and disadvantages of strategies rebuilding the lid region. The main shortcomings of biotechnologies on lid rebuilding were discussed such as negative effects on lipase (e.g., a decrease of activity). Additionally, the main shortcomings (e.g., enzyme desorption at high temperatre) in immobilization on hydrophobic supports via interfacial action were presented. Solutions to the mentioned problems were proposed by combinations of computational design with biotechnologies, and improvements of lipase immobilization (e.g., immobilization protocols and support design). Finally, the review provides future perspectives about designing hyperfunctional lipases as biocatalysts in the food industry based on lid conformation and dynamics.

Studying the effects of high pressure-temperature treatment on the structure and immunoreactivity of β-lactoglobulin using experimental and computational methods

The effects of high hydrostatic pressure (HHP) on the conformation and immunoreactivity of bovine β-lactoglobulin (BLG) were studied. BLG was treated under 100-600 MPa at the temperature of 20-60 °C. The immunoglobulin E (IgE) binding ability of BLG decreased when the pressure increased from 0.1 to 200 MPa. However, the IgE binding increased with the increase in pressure from 200 to 400 MPa, followed by a gradual decrease until a pressure of 600 MPa. The IgE binding ability continuously decreased with an increase in pressure at 60 °C. The conformation of HHP-treated BLG was evaluated using fluorescence spectroscopy, circular dichroism spectroscopy and molecular dynamics (MD) simulation. Increasing the temperature and pressure promoted the unfolding of BLG, causing the disappearance of some α-helixes and some β-sheets. Based on ELISA analysis, it was revealed that HHP-termperature treatment altered the immunoreactivity of BLG by altering the structures and conformational states of BLG.

Identifying potential thyroid hormone disrupting effects among diphenyl ether structure pesticides and their metabolites in silico

The environmental and dietary pesticide exposures can cause thyroid hormones (THs) disorders, which are associated with the high incidence of thyroid diseases worldwide. The structures of diphenyl ether pesticides and their metabolites are very similar to the structure of THs. Based on this, in silico molecular simulation approaches were used to predict, screen, evaluate and identify the binding interactions of 98 diphenyl ether structure pesticides and their metabolites (DEPMs) with 10 THs related proteins in the study. The research results indicated that these DEPMs such as fluoroglycofen (FOG), rafoxanide, diclofop, ethoxyfen and difenopenten were considered to have the greater potentials to interfere with the related proteins of THs biosynthesis, blood transport, receptor binding and metabolism. And FOG can interact with thyroid hormone receptor beta (TRβ) to form non-bond interactions. Furthermore, the results of molecular dynamics simulations showed that there were strong and stable interactions between FOG and TRβ. These results suggested that the herbicide FOG was likely to disturb THs nuclear receptor. And benzene rings and hydrophobic groups might be the characteristic chemical functional groups for DEPMs to disrupt TRβ. The relevant results of this study can be used to provide references for environmental toxicology evaluation, food safety risk assessment, and formulation and revision of pesticides and their metabolites residue limits in agricultural products and food.

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.

In silico analysis of novel dipeptidyl peptidase-IV inhibitory peptides released from Macadamia integrifolia antimicrobial protein 2 (MiAMP2) and the possible pathways involved in diabetes protection

The aim of the present study was to screen novel dipeptidyl peptidase IV (DPP-IV) inhibitory peptides from Macadamia integrifolia antimicrobial protein 2 (MiAMP2) and evaluate the potential antidiabetic targets and involved signaling pathways using in silico approaches. In silico digestion of MiAMP2 with pepsin, trypsin and chymotrypsin was performed with ExPASy PeptideCutter and the generated peptides were subjected to BIOPEP-UWM, iDrug, INNOVAGEN and Autodock Vina for further analyses. Six novel peptides EQVR, EQVK, AESE, EEDNK, EECK, and EVEE were predicted to possess good DPP-IV inhibitory potentials, water solubility, and absorption, distribution, metabolism, excretion, and toxicity properties. Molecular dynamic simulation and molecular docking displayed that AESE was the most potent DPP-IV inhibitory peptide and can bind with the active sites of DPP-IV through hydrogen bonding and van der Waals forces. The potential antidiabetic targets of AESE were retrieved from SwissTargetPrediction and GeneCards databases. Protein-protein interaction analysis identified BIRC2, CASP3, MMP7 and BIRC3 to be the hub targets. Moreover, the KEGG pathway enrichment analysis showed that AESE prevented diabetes through the apoptosis and TNF signaling pathways. These results will provide new insights into utilization of MiAMP2 as functional food ingredients for the prevention and treatment of diabetes.

Computational strategies for the discovery of biological functions of health foods, nutraceuticals and cosmeceuticals: a review

Scientific and consumer interest in healthy foods (also known as functional foods), nutraceuticals and cosmeceuticals has increased in the recent years, leading to an increased presence of these products in the market. However, the regulations across different countries that define the type of claims that may be made, and the degree of evidence required to support these claims, are rather inconsistent. Moreover, there is also controversy on the effectiveness and biological mode of action of many of these products, which should undergo an exhaustive approval process to guarantee the consumer rights. Computational approaches constitute invaluable tools to facilitate the discovery of bioactive molecules and provide biological plausibility on the mode of action of these products. Indeed, methodologies like QSAR, docking or molecular dynamics have been used in drug discovery protocols for decades and can now aid in the discovery of bioactive food components. Thanks to these approaches, it is possible to search for new functions in food constituents, which may be part of our daily diet, and help to prevent disorders like diabetes, hypercholesterolemia or obesity. In the present manuscript, computational studies applied to this field are reviewed to illustrate the potential of these approaches to guide the first screening steps and the mechanistic studies of nutraceutical, cosmeceutical and functional foods.

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

Molecular dynamics (MD) simulation has proved to be a powerful tool in the study of proteins, nucleic acids, lipids, and carbohydrates et al. in fields of health, nutrition, and food science. In particular, MD simulation has been employed in the investigation of various lipid systems such as triglycerides, phospholipid membranes, etc. Due to the continuous updating of computing resources and the development of new MD simulation methods and force field parameters, the simulation's time and size scale of lipids system has increased by several orders of magnitude. However, MD simulation cannot be used for systems invovle chemical reactions. These greatly limit its further application in the field of lipid research. This paper reviews the progress and development of MD simulation, especially for the application of MD simulation in different lipid systems. In this paper, MD simulation and its general workflow was briefly introduced firstly. Subsequently, the application of MD simulation in various lipid systems was reviewed in-depth. Finally, the limitation and future prospects of MD simulation in lipid research were also discussed. This review provided new insights into the investigation of MD simulation, and a novel thought for lipid study. We believe that MD simulation will exhibit more and more great advantages in the investigation of lipids in the future due to the development of novlel methods.

Double-crosslinked effect of TGase and EGCG on myofibrillar proteins gel based on physicochemical properties and molecular docking

The aim of this study was to determine the influence and mechanism of combining EGCG with TGase on properties of myofibrillar protein (MP) gel. A double-crosslinked effect was observed when EGCG and TGase were added into MP gel. Breaking force, deformation, water holding capacity and hardness of double-crosslinked MP gel increased by 25.3 ± 3.0 g, 0.5 ± 0.3 mm, 1.76 ± 0.4% and 34.11 ± 2.56 g, compared with those of TGase induced gel. Light microscopy and low-field nuclear magnetic resonance results indicated with EGCG content increasing, pores and structure of double-crosslinked gels became smaller and denser, T₂₂ decreased from 266.162 ms to 252.845 ms and its proportion increased from 94.103% to 96.956%. Molecular docking illustrated covalent and non-covalent interactions between EGCG and myosin heavy chain Ⅱ A, and confirmed TGase catalytic mechanism with myosin heavy chain Ⅱ A as substrate. Therefore the mixture of EGCG and TGase could be used as novel cross-linker in surimi.

Structural and functional changes of the protein β-lactoglobulin under thermal and electrical processing conditions

In the present study we have tried to explore the effect of static external electric field of strength 3.0 V/nm on the conformational changes adopted by the protein β-lactoglobulin. We have chosen different temperatures viz. 300 K, 400 K and 450 K to evaluate the temperature dependent effect of electric field. We have observed that combined effect of high temperature and static external electric field show significant changes on the structural conformation of the protein which in turn may affect the functional properties of the protein. Calculations of root mean square deviations reveal that both helical and β-sheet regions of the protein are noticeably affected at high temperature. We have used solvent accessible surface area (SASA) and dipole moment values to explain that there is changes in hydrophobicity of the protein surface due to presence of external electric field. The study reveals that electric field in combination with high temperature can be used to alter the conformation of the protein and the effect of external electric field is more pronounced at high temperature than that of low temperature. The study provides a better understanding of the conformational changes adopted by the protein under the stress of external electric field and high temperature and provide guidance to choose optimum conditions for processing without loss of nutritional properties.

Heteroprotein complex coacervation: Focus on experimental strategies to investigate structure formation as a function of intrinsic and external physicochemical parameters for food applications

Proteins are important components of foods, because they are one of the essential food groups, they have many functional properties that are very useful for modifying the physicochemical and textural properties of processed foods and possess many biological activities that are beneficial to human health. The process of heteroprotein complex coacervation (HPCC) combines two or more proteins through long-range coulombic interaction and specific short-range forces, creating a liquid-liquid colloid, with highly concentrated protein in the droplet phase and much more diluted-protein in the bulk phase. Coacervates possess novel, modifiable, physicochemical characteristics, and often exhibit the combined biological activities of the protein components, which makes them applicable to formulated foods and encapsulation carriers. This review discusses research progress in the field of HPCC in three parts: (1) the basic and innovative experimental methods and simulation tools for understanding the physicochemical behavior of these heteroprotein supramolecular architectures; (2) the influence of environmental factors (pH, mixing ratio, salts, temperature, and formation time) and intrinsic factors (protein modifications, metal-binding, charge anisotropy, and polypeptide designs) on HPCC; (3) the potential applications of HPCC materials, such as encapsulation of nutraceuticals, nanogels, emulsion stabilization, and protein separation. The wide diversity of possible combinations of proteins with different properties, endows HPCC materials with great potential for development into highly-innovation functional food ingredients.

Interactions between cell wall polysaccharides and polyphenols: Effect of molecular internal structure

Cell wall polysaccharides (CPSs) and polyphenols are major constituents of the dietary fiber complex in plant-based foods. Their digestion (by gut microbiota) and bioefficacy depend not only on their structure and quantity, but also on their intermolecular interactions. The composition and structure of these compounds vary with their dietary source (i.e., fruit or vegetable of origin) and can be further modified by food processing. Various components and structures of CPSs and polyphenols have been observed to demonstrate common and characteristic behaviors during interactions. However, at a fundamental level, the mechanisms that ultimately drive these interactions are still not fully understood. This review summarizes the current state of knowledge on the internal factors that influence CPS-polyphenol interactions, describes the different ways in which these interactions can be mediated by molecular composition or structure, and introduces the main methods for the analysis of these interactions, as well as the mechanisms involved. Furthermore, a comprehensive overview is provided of recent key findings in the area of CPS-polyphenol interactions. It is becoming clear that these interactions are shaped by a multitude of factors, the most important of which are the physicochemical properties of the partners: their morphology (surface area and porosity/pore shape), chemical composition (sugar ratio, solubility, and non-sugar components), and molecular architecture (molecular weight, degree of esterification, functional groups, and conformation). An improved understanding of the molecular mechanisms that drive interactions between CPSs and polyphenols may allow us to better establish a bridge between food processing and the bioavailability of colonic fermentation products from CPSs and antioxidant polyphenols, which could ultimately lead to the development of new guidelines for the design of healthier and more nutritious foods.

Sensorial Perception of Astringency: Oral Mechanisms and Current Analysis Methods

Understanding consumers' food choices and the psychological processes involved in their preferences is crucial to promote more mindful eating regulation and guide food design. Fortifying foods minimizing the oral dryness, rough, and puckering associated with many functional ingredients has been attracting interest in understanding oral astringency over the years. A variety of studies have explored the sensorial mechanisms and the food properties determining astringency perception. The present review provides a deeper understanding of astringency, a general view of the oral mechanisms involved, and the exciting variety of the latest methods used to direct and indirectly quantify and simulate the astringency perception and the specific mechanisms involved.

Heat-Stable Hazelnut Profilin: Molecular Dynamics Simulations and Immunoinformatics Analysis

Heat treatment can modify the allergenic potential, reducing allergenicity in specific proteins. Profilins are one of the important hazelnut allergens; these proteins are considered panallergens due to their high capacity for cross-reactivity with other allergens. In the present work, we evaluated the thermostability of hazelnut profilin, combining molecular dynamics simulation and immunoinformatic techniques. This approach helped us to have reliable results in immunogenicity studies. We modeled Cor a 2 profilin and applied annealing simulation, equilibrium, and production simulation at constant temperatures ranging from 300 to 500 K using Gromacs software. Despite the hazelnut profilins being able to withstand temperatures of up to 400 K, this does not seem to reduce its allergenicity. We have found that profilin subjected to temperatures of 450 and 500 K could generate cross-reactivity with other food allergens. In conclusion, we note a remarkable thermostability of Cor a 2 at 400 K which avoids its structural unfolding.

Assessment of the endocrine-disrupting effects of diethyl phosphate, a nonspecific metabolite of organophosphorus pesticides, by in vivo and in silico approaches

Organophosphorus pesticides (OPs) remain one of the most commonly used pesticides, and their detection rates and residues in agricultural products, foods and environmental samples have been underestimated. Humans and environmental organisms are at high risk of exposure to OPs. Most OPs can be degraded and metabolized into dialkyl phosphates (DAPs) in organisms and the environment, and can be present in urine as biomarkers for exposure to OPs, of which diethyl phosphate (DEP) is a high-exposure metabolite. Epidemiological and cohort studies have found that DAPs are associated with endocrine hormone disorders, especially sex hormone disorders and thyroid hormone disorders, but there has been no direct causal evidence to support these findings. Our study explored the effects of chronic exposure to DEP on endocrine hormones and related metabolic indicators in adult male rats at actual doses that can be reached in the human body. The results showed that chronic exposure to DEP could cause thyroid-related hormone disorders in the serum of rats, causing symptoms of hyperthyroidism in rats, and could also lead to abnormal expression of thyroid hormone-related genes in the rat liver. However, DEP exposure did not seem to affect serum sex hormone levels, spermatogenesis or sperm quality in rats. The molecular interactions between DEP and thyroid hormone-related enzymes/proteins were investigated by molecular docking and molecular dynamics methods in silico. It was found that DEP could strongly interact with thyroid hormone biosynthesis, blood transport, receptor binding and metabolism-related enzymes/proteins, interfering with the production and signal regulation of thyroid hormones. In vivo and in silico experiments showed that DEP might be a potential thyroid hormone-disrupting chemical, and therefore, we need to be more cautious and rigorous regarding organophosphorus chemical exposure.

Mechanism of binding interactions between young apple polyphenols and porcine pancreatic α-amylase

The binding interactions between young apple polyphenols and porcine pancreatic α-amylase were investigated through isothermal titration calorimetry (ITC), differential scanning calorimetry (DSC) and molecular docking. The results obtained were compared with those obtained through inhibition kinetics and fluorescence quenching. It was found that binding of tannic acid, chlorogenic acid, caffeic acid and epicatechin with α-amylase is an exothermal process, with the binding constants in the order of tannic acid > chlorogenic acid > caffeic acid > epicatechin. This is consistent with the orders of reciprocal of competitive inhibition constant and fluorescence quenching constant. The binding energy obtained through molecular docking showed the same order, except for epicatechin. These results are consistent with the inhibition of α-amylase being caused by the binding of the polyphenols with the enzyme. In addition, from the fluorescence quenching and DSC data, total polyphenols, tannic acid, chlorogenic acid and caffeic acid were found to partially unfold the enzyme structure.