Simulations of Temperature and Pressure Unfolding in Soy Allergen Gly m 4 Using Molecular Modeling

Effect of high hydrostatic pressure treatment on food composition and applications in food industry: A review

Nowadays, with the diversification of nutritious and healthy foods, consumers are increasingly seeking clean-labeled products. High hydrostatic pressure (HHP) as a cold sterilization technology can effectively sterilize and inactivate enzymes, which is conducive to the production of high-quality and safe food products with extended shelf life. This technology reduces the addition of food additives and contributes to environmental protection. Moreover, HHP enhances the content and bioavailability of nutrients, reduces the anti-nutritional factors and the risk of food allergen concerns. Therefore, HHP is widely used in the processing of fruit and vegetable juice drinks, alcoholic, meat products and aquatic products, etc. A better understanding of the influence of HHP on food composition and applications can guide the development of food industry and contribute to the development of non-thermally processed and environmentally friendly foods.

Techno-Functions and Safety Concerns of Plant-Based Peptides in Food Matrices

Plant-based peptides (PBPs) benefit functional food development and environmental sustainability. Proteolysis remains the primary method of peptide production because it is a mild and nontoxic technique. However, potential safety concerns still emanate from toxic or allergenic sequences, amino acid racemization, iso-peptide bond formation, Maillard reaction, dose usage, and frequency. The main aim of this review is to investigate the techno-functions of PBPs in food matrices, as well as their safety concerns. The distinctive characteristics of PBPs exhibit their techno-functions for improving food quality and functionality by contributing to several crucial food formulations and processing. The techno-functions of PBPs include solubility, hydrophobicity, bitterness, foaming, oil-binding, and water-holding capacities, which subsequently affect food matrices. The safety and quality of foodstuff containing PBPs depend on the proper source of plant proteins, the selection of processing approaches, and compliance with legal regulations for allergen labeling and safety evaluations. The safety concerns in allergenicity and toxicity were discussed. The conclusion is that food technologists must apply safe limits and consider potential allergenic components generated during the development of food products with PBPs. Therefore, functional food products containing PBPs can be a promising strategy to provide consumers with wholesome health benefits.

Dairy, Plant, and Novel Proteins: Scientific and Technological Aspects

Alternative proteins have gained popularity as consumers look for foods that are healthy, nutritious, and sustainable. Plant proteins, precision fermentation-derived proteins, cell-cultured proteins, algal proteins, and mycoproteins are the major types of alternative proteins that have emerged in recent years. This review addresses the major alternative-protein categories and reviews their definitions, current market statuses, production methods, and regulations in different countries, safety assessments, nutrition statuses, functionalities and applications, and, finally, sensory properties and consumer perception. Knowledge relative to traditional dairy proteins is also addressed. Opportunities and challenges associated with these proteins are also discussed. Future research directions are proposed to better understand these technologies and to develop consumer-acceptable final products.

Characterization of T-Cell Epitopes in Food Allergens by Bioinformatic Tools

The identification of T-cell epitopes is a critical step in the understanding of the immunologic mechanisms such as food allergy. Epitope screening in silico by bioinformatic tools can be used to identify T-cell epitopes, which can save time and resources. In this chapter, a multiparametric approach to predict and assess major histocompatibility complex (MHC) class II binding T-cell epitopes using bioinformatics was introduced for food allergens. Furthermore, the ability of predicted T-cell epitopes to induce interleukin (IL)-4, as well as the allergenicity potential based on the sequence analysis and population coverage of epitopes were also determined. The molecular docking approach was further used to explore the binding ability between epitopes and human leukocyte antigen (HLA) class II molecules. The amino acids that might be responsible for binding to HLA class II molecules and their binding interactions were analyzed.

Identification and Verification of Novel Umami Peptides Isolated from Hybrid Sturgeon Meat (Acipenser baerii × Acipenser schrenckii)

To explore the umami mechanism in sturgeon meat, five peptides (ERRY, VRGPR, LKYPLE, VKKVFK, and YVVFKD) were isolated and identified by ultrafiltration, gel filtration chromatography, and UPLC-QTOF-MS/MS. The omission test confirmed that the five umami peptides contributed to the umami taste of sturgeon meat. Also, the peptides had the double effective role of enhancing both umami and saltiness. The threshold of ERRY was only 0.031, which exceeded most umami peptides in the last 3 years. Molecular docking results showed that five peptides could easily bind to Gly167, Ser170, and Try218 residues in T1R3 through hydrogen bonds and electrostatic interactions. Furthermore, molecular dynamics simulations indicated that hydrogen bonds and hydrophobic interactions were the main intermolecular interaction forces. This study could contribute to revealing the umami taste mechanism of sturgeon meat and provide new insights for effective screening of short umami peptides.

Effects of magnetic nanoscale combined radio frequency or microwave thawing on conformation of sea bass myosin heavy chain: a molecular dynamics study

BACKGROUND

The consumption of frozen foods inevitably involves a thawing process. Protein conformation changes during a short thawing process and the quantification of their effects remains challenging. Molecular dynamics simulations can be used to evaluate the conformational changes of protein occurring in food processing.

RESULTS

In the present study, four different thawing methods were used [i.e. magnetic nanometer combined with microwave thawing (MT-Mag), magnetic nanometer combined with radio frequency thawing (RT-Mag), radio frequency thawing (RT) and microwave thawing (MT)] to change the conformation of myosin heavy chain (MHC). The results obtained showed that, compared with the fresh sample, the hydrogen bond number and radius of gyration of the RT-Mag and RT groups were less decreased. Visual molecular dynamics STRIDE analysis showed that the content of the α helix was relatively high in the RT-Mag and MT-Mag groups.

CONCLUSION

These simulation results indicate that RT-Mag can be used as an effective method for promoting the thawing process of fish and better stabilizing the protein structure. These conclusions provide a theoretical realization for understanding the protein conformational transition during the thawing process and the realization of quantification and also provide guidance for choosing better thawing conditions without loss of nutritional properties. © 2022 Society of Chemical Industry.

Investigation of the differences in the effect of (-)-epigallocatechin gallate and proanthocyanidins on the functionality and allergenicity of soybean protein isolate

In this study, the differences in effects of (-)-epigallocatechin gallate (EGCG) and proanthocyanidins (PC) on the functionality and allergenicity of soybean protein isolate (SPI) were studied. SDS-PAGE demonstrated that SPI-PC conjugates exhibited more high-molecular-weight polymers (>180 kDa) than SPI-EGCG conjugates. Structural analysis showed that SPI-PC conjugates exhibited more disordered structures and protein-unfolding, improving the accessibility of PC to modify SPI, compared to SPI-EGCG conjugates. LC/MS-MS demonstrated that PC caused more modification of SPI and major soybean allergens than EGCG, resulting in a lower abundance of epitopes. The successful attachment of EGCG and PC to SPI significantly increased antioxidant capacity in conjugates. Furthermore, SPI-PC conjugates exhibited greater emulsifying activity and lower immunoglobulin E (IgE) binding capacity than SPI-EGCG conjugates, which was attributed to more disordered structure and protein-unfolding in SPI-PC conjugates. It is implied that proanthocyanidins may be promising compounds to interact with soybean proteins to produce functional and hypoallergenic foods.

Molecular dynamic (in silico) modeling of structure-function of glutelin type-B 5-like from proso millet storage protein: effects of temperature and pressure

Molecular dynamic (MD) simulation provides an insight into the behavior of a protein under applied processing at the molecular level. The behavior of glutelin type-B 5-like protein, a type of glutelin protein from proso millet was studied, in solution under different temperatures (300, 350, and 400 K) and pressure (1 bar, 3 kbar, and 6 kbar) levels using a molecular dynamics simulation approach. The combined treatment effect (400 K, 6 kbar) increased the compaction of the protein compared to the level at (300 K, 1 bar) as shown by the decreased radius of gyration values from 3.26 to 2.92 nm, decreased solvent accessibility surface area from 327.47 to 311.06 nm2 and decreased volume from 108.35 to 105.04 nm3. The root means square deviation increased with increasing temperature but decreased with increasing pressure while the root means square fluctuations increased significantly with increased in temperature and pressure. A snapshot of the three-dimensional structure of the protein revealed compression of its occluded cavities at higher pressure levels but no obvious disruption to the secondary structure elements of the protein was observed, except for the loss of a few amino acid residues that comprise the secondary structure element.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13197-022-05594-y.

C-Terminal Modification on the Immunomodulatory Activity, Antioxidant Activity, and Structure–Activity Relationship of Pulsed Electric Field (PEF)-Treated Pine Nut Peptide

In this study, a novel peptide VNAVL was synthesized by removing the C-terminal histidine on the basis of a bioactive peptide VNAVLH obtained from pine nut (Pinus koraiensis Sieb. et Zucc) protein. The effects of removing histidine on antioxidant activity, immunomodulatory activity, and secondary structure of the PEF-treated peptide were discussed. Compared with VNAVLH, VNAVL only exhibited lower antioxidant activity, but no immunomodulatory activity to release TNF-α, IL-6, and NO by activating RAW 264.7 cells. In addition, both antioxidant and immune activities of VNAVLH were significantly more sensitive to treatment with 40 kV/cm than other field intensities, whereas VNAVL was not sensitive to field strength changes. CD spectra and DSSP analysis verified that both peptides consisted of a β structure and random coil, but the ability of VNAVL to transform the random coil via PEF treatment is weaker than that of VNAVLH. Therefore, PEF treatment might expose the key active site located on the C-terminal histidine by altering the secondary structure of the peptide.

Investigation of differences in allergenicity of protein from different soybean cultivars through LC/MS-MS

Soybean allergy is a health-threatening issue and identifying raw soybeans with low allergenicity is important for producing hypoallergenic soybean products. Soybean allergy is mainly triggered by soybean proteins. In this study, the protein profiles, allergen compositions, and epitopes in protein from different soybean cultivars (R1, R2 and R3) were evaluated by SDS-PAGE and LC/MS-MS, and their allergenicity was assessed by indirect ELISA and Western blot analysis using the serum IgE of patients allergic to soybeans. The lowest allergenicity was observed in R3, probably resulting from the low concentration of Gly m 4-Gly m 6. The allergenicity of soybeans is affected by multiple allergens rather than a single allergen. Venn diagram, PCA, heatmap, and peptide map analyses have shown the differences in protein and peptide profiles among soybean proteins from different soybean cultivars. Epitope analysis further demonstrated that low contents of dominant epitopes in Gly m 4 and Gly m 5 contributed to low allergenicity in R3, although R3 contained high contents of no-dominant epitopes.

Electromagnetic bioeffects: a multiscale molecular simulation perspective

Electromagnetic bioeffects remain an enigma from both the experimental and theoretical perspectives despite the ubiquitous presence of related technologies in contemporary life. Multiscale computational modelling can provide valuable insights into biochemical systems and predict how they will be perturbed by external stimuli. At a microscopic level, it can be used to determine what (sub)molecular scale reactions various stimuli might induce; at a macroscopic level, it can be used to examine how these changes affect dynamic behaviour of essential molecules within the crowded biomolecular milieu in living tissues. In this review, we summarise and evaluate recent computational studies that examined the impact of externally applied electric and electromagnetic fields on biologically relevant molecular systems. First, we briefly outline the various methodological approaches that have been employed to study static and oscillating field effects across different time and length scales. The practical value of such modelling is then illustrated through representative case-studies that showcase the diverse effects of electric and electromagnetic field on the main physiological solvent - water, and the essential biomolecules - DNA, proteins, lipids, as well as some novel biomedically relevant nanomaterials. The implications and relevance of the theoretical multiscale modelling to practical applications in therapeutic medicine are also discussed. Finally, we summarise ongoing challenges and potential opportunities for theoretical modelling to advance the current understanding of electromagnetic bioeffects for their modulation and/or beneficial exploitation in biomedicine and industry.

Structure basis of the caffeic acid O-methyltransferase from Ligusiticum chuanxiong to understand its selective mechanism

Caffeic acid O-methyltransferase from Ligusticum chuanxiong (LcCOMT) showed strict regiospecificity despite a relative degree of preference. Compared with caffeic acid, methyl caffeate was the preferential substrate by its low Km and high Kcat. In this study, we obtained the SAM binary (1.80 Å) and SAH binary (1.95 Å) complex LcCOMT crystal structures, and established the ternary complex structure with methyl caffeate by molecular docking. The active site of LcCOMT included phenolic substrate pocket, SAM/SAH ligand pocket and conserved catalytic residues as well. The regiospecificity of LcCOMT that permitted only 3-hydroxyl group to be methylated arise from the interactions between the active site and the phenyl ring. However, the propanoid tail governed the relative preference of LcCOMT. The ester group in methyl caffeate stabilized the anionic intermediate caused by His268-Asp269 pair, whereas caffeic acid was unable to stabilize the anionic intermediate due to the adjacent carboxylate anion in the propanoid tail. Ser183 residue formed an additional hydrogen bond with SAH and its role was identified by S183A mutation. Ile318 residue might be a potential site for determination of substrate preference, and its mutation led to the change of tertiary conformation. The results supported the selective mechanism of LcCOMT.

Effect of high hydrostatic pressure on the edible quality, health and safety attributes of plant-based foods represented by cereals and legumes: a review

Consumers today are increasingly willing to reduce their meat consumption and adopt plant-based alternatives in their diet. As a main source of plant-based foods, cereals and legumes (CLs) together could make up for all the essential nutrients that humans consume daily. However, the consumption of CLs and their derivatives is facing many challenges, such as the poor palatability of coarse grains and vegetarian meat, the presence of anti-nutritional factors, and allergenic proteins in CLs, and the vulnerability of plant-based foods to microbial contamination. Recently, high hydrostatic pressure (HHP) technology has been used to tailor the techno-functionality of plant proteins and induce cold gelatinization of starch in CLs to improve the edible quality of plant-based products. The nutritional value (e.g., the bioavailability of vitamins and minerals, reduction of anti-nutritional factors of legume proteins) and bio-functional properties (e.g., production of bioactive peptides, increasing the content of γ-aminobutyric acid) of CLs were significantly improved as affected by HHP. Moreover, the food safety of plant-based products could be significantly improved as well. HHP lowered the risk of microbial contamination through the inactivation of numerous microorganisms, spores, and enzymes in CLs and alleviated the allergy symptoms from consumption of plant-based foods.

Do non-thermal effects exist in microwave heating of glucose aqueous solutions? Evidence from molecular dynamics simulations

The existence of microwave non-thermal effects in food processing is still debated. In this study, molecular dynamics (MD) simulations were performed to investigate the conformation, electrostatic profiles, and intramolecular hydrogen bonds (intra-HB) of glucose in aqueous solution under alternating electric fields of microwaves ranging from 0 to 10⁹ V/m at 2.45 GHz. The results showed a field-induced threshold of 10⁹ V/m. At the threshold, alternating microwaves reoriented the flexible moieties and thus enhanced the intra-HB. The conformational transition among gg, gt, and tg conformers at 10⁹ V/m possibly resulted from the uneven electrostatic potential and the increased intra-HB. In practice, the maximum electric field of microwaves is several times weaker than the threshold, verifying the absence of microwave non-thermal effects for glucose molecules in food processing. This study provides a novel strategy to evaluate the potential non-thermal effects of microwaves in food processing and the related underlying food safety issues.

Protein profile of commercial soybean milks analyzed by label-free quantitative proteomics

The consumption of soy milk is increasing worldwide for its nutritional value and health benefits, however, its protein composition after commercialization is not well known. Technological and thermal treatments to which soy milk is subjected could affect the protein composition of the commercial products. This study compared the protein profile of 15 different commercial soy milks using a label-free quantitative proteomics approach. Proteins related to nutrient reservoir activity, endopeptidase inhibitor activity, lipid binding, and seed maturation contribute the most in terms of percentage mass. Their associated Gene Ontology terms are also enriched. Samples clustered into three groups based on their protein composition, with glycinins and beta-conglycinins being the most influential for determining the clustering. Amino acid composition estimated from the proteomics data also reflects the clustering of samples. Twenty allergenic proteins varying in abundance were identified, with Gly m 5 and Gly m 6 being the predominantly abundant allergens.

Internal cavity amplification of shell-like ferritin regulated with the change of the secondary and tertiary structure induced by PEF technology

In this study, the effect of pulsed electric field (PEF) on apparent morphology and molecular structure of shell-like ferritin obtained from horse spleen was determined by circular dichroic (CD), fluorescence spectroscopy, Raman spectroscopy, cold field emission scanning electron microscopy (CF-SEM) and transmission electron microscopy (TEM), and verified by molecule dynamics (MD) simulation. After PEF treatment, the α-helix content of the samples reached a minimum value at 10 kV/cm, which indicated that the ferritin structure has been partially unfolded. However, the α-helix content peaked again after resting for 2 h at 25 ± 1 °C. This indicated that the PEF-treated ferritin tended to restore its original spherical morphology probably owing to the reversible assembly characteristic of ferritin. In addition, microstructure analysis revealed that ferritin particles aggregated after PEF treatment. Therefore, PEF treatment could induce the "exposure" of hydrophobic amino acids and conversion of disulfide bond configuration, and consequently, regulate the internal cavity stability of ferritin. The research will be beneficial to expand the application of PEF treatment in the modification of protein structure, and provide a theoretical basis for the application of ferritin as a carrier of bioactive molecules in food.

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.

Use of a combination of the MD simulations and NMR spectroscopy to determine the regulatory mechanism of pulsed electric field (PEF) targeting at C-terminal histidine of VNAVLH

In this study, the targeted regulatory mechanism of pulsed electric field (PEF) was explored for antioxidant activity improvement in four peptides, RGAVIH, RGAVLH, VNAVIH, and VNAVLH, of the pine nut (Pinus koraiensis Sieb. et Zucc). The VNAVLH peptide exhibited the best antioxidant activity and the β-sheet content decreased to a minimum value at 40 kV/cm. Moreover, the chemical shifts of hydrogen atoms of 2-H Asn and 6-H His shifted to a higher magnetic field. The connectivity between N_αH (3.62 ppm) and C_αH (8.10 ppm) of 6-His residue disappeared in PEF-treated peptide. Molecule dynamics (MD) simulation verified that the distances of N_α(H₇₈)-C_α(H₈₀) and H₈₂-O₉₄ increased, whereas -OH and -C_β(H₈₃) got closer in histidine residue after applying the electric field force. Therefore, the antioxidant activity enhancement of VNAVLH might due to the targeted regulation of PEF treatment on N_αH-C_αH and imidazole group in histidine.

Structural and functional relationship of Cassia obtusifolia trypsin inhibitor to understand its digestive resistance against Pieris rapae

Although digestive resistance of Kunitz protease inhibitors has been reported extensively, the molecular mechanism is not well established. In the present study, the first X-ray structure of Cassia obtusifolia trypsin inhibitor (COTI), a member of Kunitz protease inhibitors, was solved at a resolution of 1.9 Å. The structure adopted a classic β-trefoil fold with the inhibitory loop protruding from the hydrophobic core. The role of Phe139, a unique residue in Kunitz protease inhibitors, and Arg63 in the COTI structure was verified by F139A and R63E mutants. COTI was a specific inhibitor of bovine trypsin and the result was also verified by COTI-trypsin complex formation. Meanwhile, COTI showed equivalent inhibitory activity with that of soybean trypsin inhibitor against bovine trypsin and midgut trypsin from Pieris rapae. The F139 and R63E mutants further indicated that inhibitory specificity and efficiency of COTI were closely related to the global framework, the conformation and the amino acid composition of reactive loop. Finally, a midgut trypsin from P. rapae (PrSP40), which might be involve in the food digestion, was proposed to be a potential target of COTI and might be a promising target for future crop-protection strategy. The results supported the digestive resistance of COTI.