Understanding and Controlling Food Protein Structure and Function in Foods: Perspectives from Experiments and Computer Simulations

Legume Allergens Pea, Chickpea, Lentil, Lupine and Beyond

PURPOSE OF THE REVIEW

In the last decade, an increasing trend towards a supposedly healthier vegan diet could be observed. However, recently, more cases of allergic reactions to plants and plant-based products such as meat-substitution products, which are often prepared with legumes, were reported. Here, we provide the current knowledge on legume allergen sources and the respective single allergens. We answer the question of which legumes beside the well-known food allergen sources peanut and soybean should be considered for diagnostic and therapeutic measures.

RECENT FINDINGS

These "non-priority" legumes, including beans, pea, lentils, chickpea, lupine, cowpea, pigeon pea, and fenugreek, are potentially new important allergen sources, causing mild-to-severe allergic reactions. Severe reactions have been described particularly for peas and lupine. An interesting aspect is the connection between anaphylactic reactions and exercise (food-dependent exercise-induced anaphylaxis), which has only recently been highlighted for legumes such as soybean, lentils and chickpea. Most allergic reactions derive from IgE cross-reactions to homologous proteins, for example between peanut and lupine, which is of particular importance for peanut-allergic individuals ignorant to these cross-reactions. From our findings we conclude that there is a need for large-scale studies that are geographically distinctive because most studies are case reports, and geographic differences of allergic diseases towards these legumes have already been discovered for well-known "Big 9" allergen sources such as peanut and soybean. Furthermore, the review illustrates the need for a better molecular diagnostic for these emerging non-priority allergen sources to evaluate IgE cross-reactivities to known allergens and identify true allergic reactions.

Unleashing the Potential of Digitalization in the Agri-Food Chain for Integrated Food Systems

Digitalization transforms many industries, especially manufacturing, with new concepts such as Industry 4.0 and the Industrial Internet of Things. However, information technology also has the potential to integrate and connect the various steps in the supply chain. For the food industry, the situation is ambivalent: It has a high level of automatization, but the potential of digitalization is so far not used today. In this review, we discuss current trends in information technology that have the potential to transform the food industry into an integrated food system. We show how this digital transformation can integrate various activities within the agri-food chain and support the idea of integrated food systems. Based on a future-use case, we derive the potential of digitalization to tackle future challenges in the food industry and present a research agenda.

Differences between Omicron SARS-CoV-2 RBD and other variants in their ability to interact with cell receptors and monoclonal antibodies

SARS-CoV-2 remains a health threat with the continuous emergence of new variants. This work aims to expand the knowledge about the SARS-CoV-2 receptor-binding domain (RBD) interactions with cell receptors and monoclonal antibodies (mAbs). By using constant-pH Monte Carlo simulations, the free energy of interactions between the RBD from different variants and several partners (Angiotensin-Converting Enzyme-2 (ACE2) polymorphisms and various mAbs) were predicted. Computed RBD-ACE2-binding affinities were higher for two ACE2 polymorphisms (rs142984500 and rs4646116) typically found in Europeans which indicates a genetic susceptibility. This is amplified for Omicron (BA.1) and its sublineages BA.2 and BA.3. The antibody landscape was computationally investigated with the largest set of mAbs so far in the literature. From the 32 studied binders, groups of mAbs were identified from weak to strong binding affinities (e.g. S2K146). These mAbs with strong binding capacity and especially their combination are amenable to experimentation and clinical trials because of their high predicted binding affinities and possible neutralization potential for current known virus mutations and a universal coronavirus.Communicated by Ramaswamy H. Sarma.

Milk Protein Adsorption on Metallic Iron Surfaces

Food processing and consumption involves multiple contacts between biological fluids and solid materials of processing devices, of which steel is one of the most common. Due to the complexity of these interactions, it is difficult to identify the main control factors in the formation of undesirable deposits on the device surfaces that may affect safety and efficiency of the processes. Mechanistic understanding of biomolecule-metal interactions involving food proteins could improve management of these pertinent industrial processes and consumer safety in the food industry and beyond. In this work, we perform a multiscale study of the formation of protein corona on iron surfaces and nanoparticles in contact with cow milk proteins. By calculating the binding energies of proteins with the substrate, we quantify the adsorption strength and rank proteins by the adsorption affinity. We use a multiscale method involving all-atom and coarse-grained simulations based on generated ab initio three-dimensional structures of milk proteins for this purpose. Finally, using the adsorption energy results, we predict the composition of protein corona on iron curved and flat surfaces via a competitive adsorption model.

Mechanistic inhibition of Monkeypox and Marburg virus infection by O-rhamnosides and Kaempferol-o-rhamnosides derivatives: a new-fangled computational approach

The increasing incidence of Monkeypox virus (Mpox) and Marburg virus (MARV) infections worldwide presents a significant challenge to global health, as limited treatment options are currently available. This study investigates the potential of several O-rhamnosides and Kaempferol-O-rhamnosides as Mpox and MARV inhibitors using molecular modeling methods, including ADMET, molecular docking, and molecular dynamics/MD simulation. The effectiveness of these compounds against the viruses was assessed using the Prediction of Activity Spectra for Substances (PASS) prediction. The study's primary focus is molecular docking prediction, which demonstrated that ligands (L07, L08, and L09) bind to Mpox (PDB ID: 4QWO) and MARV (PDB ID: 4OR8) with binding affinities ranging from -8.00 kcal/mol to -9.5 kcal/mol. HOMO-LUMO based quantum calculations were employed to determine the HOMO-LUMO gap of frontier molecular orbitals (FMOs) and to estimate chemical potential, electronegativity, hardness, and softness. Drug similarity and ADMET prediction assessments of pharmacokinetic properties revealed that the compounds were likely non-carcinogenic, non-hepatotoxic, and rapidly soluble. Molecular dynamic (MD) modeling was used to identify the most favorable docked complexes involving bioactive chemicals. MD simulations indicate that varying types of kaempferol-O-rhamnoside are necessary for successful docking validation and maintaining the stability of the docked complex. These findings could facilitate the discovery of novel therapeutic agents for treating illnesses caused by the Mpox and MARV viruses.

Ultrasound-assisted free radical modification on the structural and functional properties of ovalbumin-epigallocatechin gallate (EGCG) conjugates

The influence of ultrasound-assisted free radical modification on the structure and functional properties of ovalbumin-epigallocatechin gallate (OVA-EGCG) conjugates was investigated by experimental measurements and computer simulations. Compared with the traditional free radical condition, the ultrasonic-assisted processing significantly increased the conjugating efficiency of OVA and EGCG and shortened the conjugating from 24 h to 1 h without affecting the equivalent amount of EGCG conjugating. The sodium dodecyl sulfate-polyacrylamide gel electrophoresis and multi-spectroscopy analysis (Fourier transform infrared spectroscopy, intrinsic fluorescence spectroscopy, and UV spectroscopy) indicated that the covalent conjugates could be formed between OVA and EGCG. And modification in the conformation of OVA was induced by EGCG. Furthermore, molecular docking results demonstrated the possession of high-affinity EGCG binding location on OVA, supporting and clarifying the experimental results. In addition, the functional properties of OVA including emulsification (emulsifying activity and emulsion stability) and antioxidant properties (DPPH scavenging capacity and ABTS scavenging capacity) were significantly improved after conjugation with EGCG, especially in ultrasound-assisted conditions. Overall, OVA-EGCG conjugates produced by ultrasound-assisted free radical treatment could be applied as a potential emulsifier and antioxidant, thereby expanding the application of OVA as a dual-functional ingredient.

Towards an optimal monoclonal antibody with higher binding affinity to the receptor-binding domain of SARS-CoV-2 spike proteins from different variants

A highly efficient and robust multiple scales in silico protocol, consisting of atomistic Molecular Dynamics (MD), coarse-grain (CG) MD, and constant-pH CG Monte Carlo (MC), has been developed and used to study the binding affinities of selected antigen-binding fragments of the monoclonal antibody (mAbs) CR3022 and several of its here optimized versions against 11 SARS-CoV-2 variants including the wild type. Totally 235,000 mAbs structures were initially generated using the RosettaAntibodyDesign software, resulting in top 10 scored CR3022-like-RBD complexes with critical mutations and compared to the native one, all having the potential to block virus-host cell interaction. Of these 10 finalists, two candidates were further identified in the CG simulations to be the best against all SARS-CoV-2 variants. Surprisingly, all 10 candidates and the native CR3022 exhibited a higher affinity for the Omicron variant despite its highest number of mutations. The multiscale protocol gives us a powerful rational tool to design efficient mAbs. The electrostatic interactions play a crucial role and appear to be controlling the affinity and complex building. Studied mAbs carrying a more negative total net charge show a higher affinity. Structural determinants could be identified in atomistic simulations and their roles are discussed in detail to further hint at a strategy for designing the best RBD binder. Although the SARS-CoV-2 was specifically targeted in this work, our approach is generally suitable for many diseases and viral and bacterial pathogens, leukemia, cancer, multiple sclerosis, rheumatoid, arthritis, lupus, and more.

A Long Journey into the Investigation of the Structure–Dynamics–Function Paradigm in Proteins through the Activities of the Palermo Biophysics Group

An overview of the biophysics activity at the Department of Physics and Chemistry Emilio Segrè of the University of Palermo is given. For forty years, the focus of the research has been on the protein structure–dynamics–function paradigm, with the aim of understanding the molecular basis of the relevant mechanisms and the key role of solvent. At least three research lines are identified; the main results obtained in collaboration with other groups in Italy and abroad are presented. This review is dedicated to the memory of Professors Massimo Ugo Palma, Maria Beatrice Palma Vittorelli, and Lorenzo Cordone, which were the founders of the Palermo School of Biophysics. We all have been, directly or indirectly, their pupils; we miss their enthusiasm for scientific research, their deep physical insights, their suggestions, their strict but always constructive criticisms, and, most of all, their friendship. This paper is dedicated also to the memory of Prof. Hans Frauenfelder, whose pioneering works on nonexponential rebinding kinetics, protein substates, and energy landscape have inspired a large part of our work in the field of protein dynamics.

Electrostatic Features for the Receptor Binding Domain of SARS-COV-2 Wildtype and Its Variants. Compass to the Severity of the Future Variants with the Charge-Rule

Electrostatic intermolecular interactions are important in many aspects of biology. We have studied the main electrostatic features involved in the interaction of the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein with the human receptor Angiotensin-converting enzyme 2 (ACE2). As the principal computational tool, we have used the FORTE approach, capable to model proton fluctuations and computing free energies for a very large number of protein-protein systems under different physical-chemical conditions, here focusing on the RBD-ACE2 interactions. Both the wild-type and all critical variants are included in this study. From our large ensemble of extensive simulations, we obtain, as a function of pH, the binding affinities, charges of the proteins, their charge regulation capacities, and their dipole moments. In addition, we have calculated the pK_as for all ionizable residues and mapped the electrostatic coupling between them. We are able to present a simple predictor for the RBD-ACE2 binding based on the data obtained for Alpha, Beta, Gamma, Delta, and Omicron variants, as a linear correlation between the total charge of the RBD and the corresponding binding affinity. This "RBD charge rule" should work as a quick test of the degree of severity of the coming SARS-CoV-2 variants in the future.

An insight into the changes in conformation and emulsifying properties of soy β-conglycinin and glycinin as affected by EGCG: Multi-spectral analysis

The binding mechanisms between soy β-conglycinin/glycinin and (-)-epigallocatechin-3-gallate (EGCG) were evaluated using multi-spectral techniques and molecular modeling. Additionally, the emulsifying properties of β-conglycinin/glycinin were investigated in their interactions with EGCG. Fluorescence analysis revealed that the quenching of β-conglycinin/glycinin by EGCG was static quenching. Specifically, EGCG to β-conglycinin/glycinin resulted in the conformation changes of the Trp and Tyr residues, around which the polarity toward more hydrophilic. The dominated binding between β-conglycinin and EGCG was hydrogen bonding, whereas was mainly hydrophobic force between glycinin and EGCG. Such affinity induced a more organized protein confirmation with decreased random coil and increased α-helix and β-structures. The docking data indicated the better affinity between glycinin and EGCG, compared to β-conglycinin. The emulsifying ability and capacity of β-conglycinin were enhanced with involvement EGCG, however no effect was found for glycinin. Our findings deliver insights in understanding of the interaction mechanisms between β-conglycinin/glycinin and EGCG.

Recent application of protein hydrolysates in food texture modification

The demand for clean labels has increased the importance of natural texture modifying ingredients. Proteins are unique compounds that can impart unique textural and structural changes in food. However, lack of solubility and extensive aggregability of proteins have increased the demand for enzymatically hydrolyzed proteins, to impart functional and structural modifications to food products. The review elaborates the recent application of various proteins, protein hydrolysates, and their role in texture modification. The impact of protein hydrolysates interaction with other food macromolecules, the effect of pretreatments, and dependence of various protein functionalities on textural and structural modification of food products with controlled enzymatic hydrolysis are explained in detail. Many researchers have acknowledged the positive effect of enzymatically hydrolyzed proteins on texture modification over natural protein. With enzymatic hydrolysis, various textural properties including foaming, gelling, emulsifying, water holding capacity have been effectively improved. It is evident that each protein is unique and imparts exceptional structural changes to different food products. Thus, selection of protein requires a fundamental understanding of its structure-substrate property relation. For wider applicability in the industrial sector, more studies on interactions at the molecular level, dosage, functionality changes, and sensorial attributes of protein hydrolysates in food systems are required.

Multiscale Approach to Dairy Products Design

Dairy products are among the most popular nutritious foods in the world. Understanding the relationship between the composition, process, and structural properties at different scales (molecular, microscopic, and macroscopic) is fundamental to designing dairy products. This review highlights the need to analyze this relationship from different scales as an essential step during product design through a multiscale approach.

Functional Performance of Plant Proteins

Increasingly, consumers are moving towards a more plant-based diet. However, some consumers are avoiding common plant proteins such as soy and gluten due to their potential allergenicity. Therefore, alternative protein sources are being explored as functional ingredients in foods, including pea, chickpea, and other legume proteins. The factors affecting the functional performance of plant proteins are outlined, including cultivars, genotypes, extraction and drying methods, protein level, and preparation methods (commercial versus laboratory). Current methods to characterize protein functionality are highlighted, including water and oil holding capacity, protein solubility, emulsifying, foaming, and gelling properties. We propose a series of analytical tests to better predict plant protein performance in foods. Representative applications are discussed to demonstrate how the functional attributes of plant proteins affect the physicochemical properties of plant-based foods. Increasing the protein content of plant protein ingredients enhances their water and oil holding capacity and foaming stability. Industrially produced plant proteins often have lower solubility and worse functionality than laboratory-produced ones due to protein denaturation and aggregation during commercial isolation processes. To better predict the functional performance of plant proteins, it would be useful to use computer modeling approaches, such as quantitative structural activity relationships (QSAR).

Integration of Molecular Docking Analysis and Molecular Dynamics Simulations for Studying Food Proteins and Bioactive Peptides

In silico tools, such as molecular docking, are widely applied to study interactions and binding affinity of biological activity of proteins and peptides. However, restricted sampling of both ligand and receptor conformations and use of approximated scoring functions can produce results that do not correlate with actual experimental binding affinities. Molecular dynamics simulations (MDS) can provide valuable information in deciphering functional mechanisms of proteins/peptides and other biomolecules, overcoming the rigid sampling limitations in docking analysis. This review will discuss the information related to the traditional use of in silico models, such as molecular docking, and its application for studying food proteins and bioactive peptides, followed by an in-depth introduction to the theory of MDS and description of why these molecular simulation techniques are important in the theoretical prediction of structural and functional dynamics of food proteins and bioactive peptides. Applications, limitations, and future prospects of MDS will also be discussed.

Effect of Processing on the Structure and Allergenicity of Peanut Allergen Ara h 2 Roasted in a Matrix

Peanut allergy is the leading pediatric food allergy. Many attempts have been made to reduce its allergenicity by processing. After roasting, Ara h 2 and its derivatives in the matrix were isolated by immunoaffinity chromatography (IAC). The structure and allergenicity of Ara h 2 were analyzed by circular dichroism, mass spectrometry (MS), western blotting, the enzyme-linked immunoassay, and cell modeling. Our results showed that a large portion of Ara h 2 was fragmented and cross-linked. Ara h 2 monomers accounted for only 13% of the total proteins after IAC purification. In addition, the structure of Ara h 2 changed after roasting. In addition to methylation and oxidation modification, the disulfide bonds of Ara h 2 were found to be rearranged after roasting. In the conformational structure of Ara h 2, the content of the α-helix decreased from 27.1 to 21.6% after roasting, while the content of the random coil increased from 29.1 to 34.3%. Six cleavage sites of trypsin were exposed, while three were covered. In terms of allergenicity, most of the cross-linking products were not recognized by patients' sera. Only one faint band around 40 kDa was observed in our blotting. For Ara h 2 monomers, roasting enhanced their IgE binding capacity and ability to stimulate the degranulation of basophils. The potential allergenicity increase of Ara h 2 monomers did not reflect the allergenicity change of Ara h 2 in the matrix due to the amount and property of its derivatives after roasting.

Up State of the SARS-COV-2 Spike Homotrimer Favors an Increased Virulence for New Variants

The COVID-19 pandemic has spread worldwide. However, as soon as the first vaccines-the only scientifically verified and efficient therapeutic option thus far-were released, mutations combined into variants of SARS-CoV-2 that are more transmissible and virulent emerged, raising doubts about their efficiency. This study aims to explain possible molecular mechanisms responsible for the increased transmissibility and the increased rate of hospitalizations related to the new variants. A combination of theoretical methods was employed. Constant-pH Monte Carlo simulations were carried out to quantify the stability of several spike trimeric structures at different conformational states and the free energy of interactions between the receptor-binding domain (RBD) and angiotensin-converting enzyme II (ACE2) for the most worrying variants. Electrostatic epitopes were mapped using the PROCEEDpKa method. These analyses showed that the increased virulence is more likely to be due to the improved stability to the S trimer in the opened state, in which the virus can interact with the cellular receptor, ACE2, rather than due to alterations in the complexation RBD-ACE2, since the difference observed in the free energy values was small (although more attractive in general). Conversely, the South African/Beta variant (B.1.351), compared with the SARS-CoV-2 wild type (wt), is much more stable in the opened state with one or two RBDs in the up position than in the closed state with three RBDs in the down position favoring the infection. Such results contribute to understanding the natural history of disease and indicate possible strategies for developing new therapeutic molecules and adjusting the vaccine doses for higher B-cell antibody production.

Protein deamidation to produce processable ingredients and engineered colloids for emerging food applications

With the ever-increasing demands for functional and sustainable foods from the general public, there is currently a paradigm shift in the food industry toward the production of novel protein-based diet. Food scientists are therefore motivated to search for natural protein sources and innovative technologies to modify their chemical structure for desirable functionality and thus utilization. Deamidation is a viable, efficient, and attractive approach for modifying proteins owing to its ease of operating, specificity, and cost-effective processes. Over the past three decades, the knowledge of protein deamidation for food applications has evolved drastically, including the development of novel approaches for deamidation, such as protein-glutaminase and ion exchange resin, and their practices in new protein substrate. Thanks to deamidation, enhanced functionalities of food proteins from cereals, legumes, milk, oil seeds and others, and thereby their processabilities as food ingredients have been achieved. Moreover, deamidated proteins have been used to fabricate engineered food colloids, including self-assembled protein particles, protein-metallic complexes, and protein-carbohydrate complexes, which have demonstrated tailored physicochemical properties to modulate oral perception, improve gastrointestinal digestion and bioavailability, and protect and/or deliver bioactive nutrients. Novel bioactivity, altered digestibility, and varied allergenicity of deamidated proteins are increasingly recognized. Therefore, deamidated proteins with novel techno-functional and biological properties hold both promise and challenges for future food applications, and a comprehensive review on this area is critically needed to update our knowledge and provide a better understanding on the protein deamidation and its emerging applications.

"Water Association" Band in Saccharide Amorphous Matrices: Role of Residual Water on Bioprotection

Saccharides protect biostructures against adverse environmental conditions mainly by preventing large scale motions leading to unfolding. The efficiency of this molecular mechanism, which is higher in trehalose with respect to other sugars, strongly depends on hydration and sugar/protein ratio. Here we report an Infrared Spectroscopy study on dry amorphous matrices of the disaccharides trehalose, maltose, sucrose and lactose, and the trisaccharide raffinose. Samples with and without embedded protein (Myoglobin) are investigated at different sugar/protein ratios, and compared. To inspect matrix properties we analyse the Water Association Band (WAB), and carefully decompose it into sub-bands, since their relative population has been shown to effectively probe water structure and dynamics in different matrices. In this work the analysis is extended to investigate the structure of protein-sugar-water samples, for the first time. Results show that several classes of water molecules can be identified in the protein and sugar environment and that their relative population is dependent on the type of sugar and, most important, on the sugar/protein ratio. This gives relevant information on how the molecular interplay between residual waters, sugar and protein molecules affect the biopreserving properties of saccharides matrices.

Delineating the interaction mechanism of glabridin and ovalbumin by spectroscopic and molecular docking techniques

The interaction between ovalbumin (OVA) and isoflavonoid glabridin (GB) was investigated using spectroscopic and molecular docking techniques. Fluorescence spectroscopy revealed that GB was bound to OVA mainly due to hydrogen bonding and hydrophobic forces. FT-IR spectroscopy showed that the combination of GB and OVA resulted in a decrease in the β-sheet content of OVA and an increase in the α-helix and extended-chain content. All these experimental results were supported and clarified by molecular docking simulations. GB binding was able to inhibit chemical denaturant-induced structural changes in OVA as observed by intrinsic tryptophan and ANS fluorescence. Moreover, GB-OVA complex increased the aqueous solubility of GB by about 4.45 times at pH 7.0. These results provided insights into the interaction between GB and OVA that contributes to the utilization of GB in the food and pharmaceutical industries.

Protein-polyphenol functional ingredients: The foaming properties of lactoferrin are enhanced by forming complexes with procyanidin

The solution turbidity and intrinsic fluorescence quenching increased after procyanidin was mixed with lactoferrin. The addition of procyanidin also caused a reduction in the surface hydrophobicity of the lactoferrin, suggesting procyanidin bound to non-polar patches on lactoferrin's surfaces. Moreover, the binding interaction caused an appreciable alteration in the structure of both the polyphenol and protein. Thermodynamic analysis indicated the interaction was spontaneous and mainly driven by entropy changes, suggesting that hydrophobic interactions dominated. A computational docking simulation provided insights into the location of the most-likely binding sites on the protein, as well as the nature of the interaction forces involved. In particular, both hydrophobic and hydrogen bonding were found to be important. The binding of the procyanidin to the lactoferrin enhanced its foaming properties. These results may lead to the development of a new class of natural functional ingredients that can be used in food products to improve their quality attributes.

On the interactions of the receptor-binding domain of SARS-CoV-1 and SARS-CoV-2 spike proteins with monoclonal antibodies and the receptor ACE2

A new betacoronavirus named SARS-CoV-2 has emerged as a new threat to global health and economy. A promising target for both diagnosis and therapeutics treatments of the new disease named COVID-19 is the coronavirus (CoV) spike (S) glycoprotein. By constant-pH Monte Carlo simulations and the PROCEEDpKa method, we have mapped the electrostatic epitopes for four monoclonal antibodies and the angiotensin-converting enzyme 2 (ACE2) on both SARS-CoV-1 and the new SARS-CoV-2 S receptor binding domain (RBD) proteins. We also calculated free energy of interactions and shown that the S RBD proteins from both SARS viruses binds to ACE2 with similar affinities. However, the affinity between the S RBD protein from the new SARS-CoV-2 and ACE2 is higher than for any studied antibody previously found complexed with SARS-CoV-1. Based on physical chemical analysis and free energies estimates, we can shed some light on the involved molecular recognition processes, their clinical aspects, the implications for drug developments, and suggest structural modifications on the CR3022 antibody that would improve its binding affinities for SARS-CoV-2 and contribute to address the ongoing international health crisis.