Modeling to Understand Plant Protein Structure-Function Relationships-Implications for Seed Storage Proteins

Comprehensive Characterization of Raw and Processed Quinoa from Conventional and Organic Farming by Label-Free Shotgun Proteomics

Quinoa is widely recognized for its exceptional nutritional properties, particularly its complete protein content. This study, for the first time, investigates the effects of processing methods (boiling and extrusion) and farming conditions (conventional and organic) on the proteomic profile. Following a label-free shotgun proteomics approach, a total of 1796 proteins were identified and quantified across all quinoa samples. Regarding processing, both boiling and extrusion produced protein extracts with lower total protein content, with the number of identified proteins decreasing from 1695 in raw quinoa to 957 in processed quinoa. Boiling led to a reduction in protein diversity and expression, while extrusion, which involves high temperatures and pressures, specifically decreased the abundance of high molecular mass proteins. Concerning cultivation practices, organic farming was associated with a broader protein diversity, especially proteins related to translation (28 vs 5%), while conventional farming showed a higher abundance of catalytic and enzymatic proteins (67 vs 46%). These findings highlight the distinct proteomic changes induced by different processing methods and farming conditions, offering valuable insights to manage quinoa's nutritional, bioactive, and functional properties across various production practices.

Digestion of food proteins: the role of pepsin

The nutritive value of a protein is determined not only by its amino acid composition, but also by its digestibility in the gastrointestinal tract. The interaction between proteins and pepsin in the gastric stage is the first step and plays an important role in protein hydrolysis. Moreover, it affects the amino acid release rates and the allergenicity of the proteins. The interaction between pepsin and proteins from different food sources is highly dependent on the protein species, composition, processing treatment, and the presence of other food components. Coagulation of milk proteins under gastric conditions to form a coagulum is a unique behavior that affects gastric emptying and further hydrolysis of proteins. The processing treatment of proteins, either from milk or other sources, may change their structure, interactions with pepsin, and allergenicity. For example, the heat treatment of milk proteins results in the formation of a looser curd in the gastric phase and facilitates protein digestion by pepsin. Heated meat proteins undergo denaturation and conformational changes that enhance the rate of pepsin digestion. This review provides new ideas for the design of food products containing high protein concentrations that optimize nutrition while facilitating low allergenicity for consumers.

Elucidating the role of compositional and processing variables in tailoring the technological functionalities of plant protein ingredients

Although various plant protein (PP) ingredients are available on the market, their application in foods is not trivial, and food companies are struggling to identify PP ingredients fitting the intended use. To fill this gap, abundant literature has appeared but data are hardly comparable due to the absence of a recognized classification of PP ingredients accounting not only for protein purity but also for the process history, and of standardised protocols for technological functionality assessment. In this review, a comprehensive analysis of comparable literature data was thus carried out to elucidate the effect of composition and processing variables on PP technological functionalities. The review presents four sections describing: (i) the approach followed for the construction of a database of PP ingredient functionalities; (ii) the composition and processing factors relevant to PP ingredients; (iii) PP ingredient functional properties and methods used for their determination; (iv) the effect of composition and processing factors on PP ingredient functionalities. This analysis showed legume proteins to present the highest solubility and interfacial properties while pseudocereal ones the highest water-holding capacity. Although pure ingredients show higher functionalities, non-protein components could contribute to interfacial properties. Alkaline extraction, isoelectric precipitation and freeze-drying is the process mostly used in academic research to obtain PP ingredients. However, other extraction, purification, and drying methods can be properly combined, resulting in specific PP ingredient functionalities. Overall, this review highlights that, besides protein purity and source, knowledge of the processing history is required to select PP ingredients with desired functionalities.

Advancing molecular understanding in high moisture extrusion for plant-based meat analogs: Challenges and perspectives

In recent years, meat analogs based on plant proteins have received increasing attention. However, the process of high moisture extrusion (HME), the method for their preparation, has not been thoroughly explored, particularly in terms of elucidating the complex interactions that occur during extrusion, which remain challenging. These interactions arise from the various ingredients added during HME, including proteins, starches, edible gums, dietary fibers, lipids, and enzymes. These ingredients undergo intricate conformational changes and interactions under extreme conditions of high temperature, pressure, and shear, ultimately forming the fibrous structure of meat analogs. This review offers a overview of these ingredients and the molecular interaction changes they undergo during the extrusion process. Additionally, it delves into the major molecular interactions such as disulfide bonding, hydrogen bonding, and hydrophobic interactions, providing detailed insights into each.

Integrating Computational Design and Experimental Approaches for Next-Generation Biologics

Therapeutic protein engineering has revolutionized medicine by enabling the development of highly specific and potent treatments for a wide range of diseases. This review examines recent advances in computational and experimental approaches for engineering improved protein therapeutics. Key areas of focus include antibody engineering, enzyme replacement therapies, and cytokine-based drugs. Computational methods like structure-based design, machine learning integration, and protein language models have dramatically enhanced our ability to predict protein properties and guide engineering efforts. Experimental techniques such as directed evolution and rational design approaches continue to evolve, with high-throughput methods accelerating the discovery process. Applications of these methods have led to breakthroughs in affinity maturation, bispecific antibodies, enzyme stability enhancement, and the development of conditionally active cytokines. Emerging approaches like intracellular protein delivery, stimulus-responsive proteins, and de novo designed therapeutic proteins offer exciting new possibilities. However, challenges remain in predicting in vivo behavior, scalable manufacturing, immunogenicity mitigation, and targeted delivery. Addressing these challenges will require continued integration of computational and experimental methods, as well as a deeper understanding of protein behavior in complex physiological environments. As the field advances, we can anticipate increasingly sophisticated and effective protein therapeutics for treating human diseases.

Unveiling the hidden reserves: allocation strategies associated with underground organs of Cerrado legumes in fire-prone savannas

The synthesis and differential allocation of reserve compounds is an important adaptive mechanism that enables species to resprout in fire-prone ecosystems. The analysis of compound allocation dynamics (differential accumulation of compounds between plant organs) provides insights into plant responses to disturbances. The aim was to quantify reserves in eight legume species from Cerrado open savannas with high fire frequency in order to investigate the patterns of allocation and distribution of compounds between leaves and underground organs, drawing ecophysiological inferences. The species were collected in 'campo sujo' areas of the Cerrado. Leaves and underground organs (xylopodium, taproot tubers) were subjected to physiological analyses. Overall, underground organs were characterised by greater deposits of carbohydrates, mainly soluble sugars, and also with the accumulation of proteins and amino acids. This suggests that nitrogen reserves, as well as carbohydrates, may have an ecophysiological function in response to fire, being allocated to the underground organs. Phenols were mainly evident in leaves, but a morphophysiological pattern was identified, where the two species with taproot tubers tended to concentrate more phenols in the underground portion compared to species with xylopodium, possibly due to functional differences between these organs. Such data allow inferring relevant ecophysiological dynamics in legumes from open savannas.

Expression of Iron Metabolism Genes Is Potentially Regulated by DOF Transcription Factors in Dendrocalamus latiflorus Leaves

Transcription factors (TFs) are crucial pre-transcriptional regulatory mechanisms that can modulate the expression of downstream genes by binding to their promoter regions. DOF (DNA binding with One Finger) proteins are a unique class of TFs with extensive roles in plant growth and development. Our previous research indicated that iron content varies among bamboo leaves of different colors. However, to our knowledge, genes related to iron metabolism pathways in bamboo species have not yet been studied. Therefore, in the current study, we identified iron metabolism related (IMR) genes in bamboo and determined the TFs that significantly influence them. Among these, DOFs were found to have widespread effects and potentially significant impacts on their expression. We identified specific DOF members in Dendrocalamus latiflorus with binding abilities through homology with Arabidopsis DOF proteins, and established connections between some of these members and IMR genes using RNA-seq data. Additionally, molecular docking confirmed the binding interactions between these DlDOFs and the DOF binding sites in the promoter regions of IMR genes. The co-expression relationship between the two gene sets was further validated using q-PCR experiments. This study paves the way for research into iron metabolism pathways in bamboo and lays the foundation for understanding the role of DOF TFs in D. latiflorus.

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.

Structural, extraction and safety aspects of novel alternative proteins from different sources

With rapid population growth and continued environmental degradation, it is no longer sustainable to rely on conventional proteins to meet human requirements. This has prompted the search for novel alternative protein sources of greater sustainability. Currently, proteins of non-conventional origin have been developed, with such alternative protein sources including plants, insects, algae, and even bacteria and fungi. Most of these protein sources have a high protein content, along with a balanced amino acid composition, and are regarded as healthy and nutritious sources of protein. While these novel alternative proteins have excellent nutritional, research on their structure are still at a preliminary stage, particularly so for insects, algae, bacteria, and fungi. Therefore, this review provides a comprehensive overview of promising novel alternative proteins developed in recent years with a focus on their nutrition, sustainability, classification, and structure. In addition, methods of extraction and potential safety factors for these proteins are summarized.

Validation of low-cost reflectometer to identify phytochemical accumulation in food crops

Diets consisting of greater quantity/diversity of phytochemicals are correlated with reduced risk of disease. This understanding guides policy development increasing awareness of the importance of consuming fruits, grains, and vegetables. Enacted policies presume uniform concentrations of phytochemicals across crop varieties regardless of production/harvesting methods. A growing body of research suggests that concentrations of phytochemicals can fluctuate within crop varieties. Improved awareness of how cropping practices influence phytochemical concentrations are required, guiding policy development improving human health. Reliable, inexpensive laboratory equipment represents one of several barriers limiting further study of the complex interactions influencing crop phytochemical accumulation. Addressing this limitation our study validated the capacity of a low-cost Reflectometer ($500) to measure phytochemical content in selected crops, against a commercial grade laboratory spectrophotometer. Our correlation results ranged from r2 = 0.81 for protein in wheat and oats to r2 = 0.99 for polyphenol content in lettuce in both the Reflectometer and laboratory spectrophotometer assessment, suggesting the Reflectometer provides an accurate accounting of phytochemical content within evaluated crops. Repeatability evaluation demonstrated good reproducibility of the Reflectometer to assess crop phytochemical content. Additionally, we confirmed large variation in phytochemical content within specific crop varieties, suggesting that cultivar is but one of multiple drivers of phytochemical accumulation. Our findings indicate dramatic nutrient variations could exist across the food supply, a point whose implications are not well understood. Future studies should investigate the interactions between crop phytochemical accumulation and farm management practices that influence specific soil characteristics.

Microalgae biomass as a conditioner and regulator of soil quality and fertility

Characteristics of an acid soil cultivated with Urochloa brizantha cv. Marandu were evaluated in relation to two types of fertilization: a conventional one, chemical based on nitrogen and potassium, and a biofertilizer, based on microalgae biomass. The results were compared among three treatments, control, conventional, and biological fertilization, with seven replications each. The study evaluated microalgae community, total carbon and nitrogen contents, mineral nitrogen, and enzymatic activity. Chlorella vulgaris showed the highest organism density, which can be explained by its rapid growth and high resistance. The highest species diversity was detected in the control 1,380,938 org cm-3 and biological 1,841,250 org cm-3 treatments, with the latter showing a higher density of cyanobacteria, especially Pseudanabaena limnetica with 394,554 org cm-3. The soil treated with chemical fertilization showed higher nitrate (9.14 mg NKg-1 NO3--N) and potassium (52.32 mg dm-3) contents. The highest levels of sulfur (21.73 mg dm-3) and iron (96.46 mgdm-3) were detected in the biological treatment. The chemical treatment showed higher activity of the enzymes acid phosphatase, acetylglucosaminidase, and sulfatase, while α-glucosidase and leucine aminopeptidase stood out in the biological treatment. Soil properties were not significantly affected by the treatments. The use of microalgae biomass derived from wastewater treatment from milking parlors was evaluated and presented as a promising biofertilizer for agriculture, following the line of recovering nutrient-rich wastes. In this sense, although many challenges need to be overcome, the results suggest that microalgal-based fertilizers could lead to low-impact agriculture.

Chemical Composition, Lipid-Soluble Bioactive Compounds and Potential Health Benefits of the Moss Hypnum cupressiforme Hedw

Hypnum cupressiforme Hedw. is the main species for Moss surveys (ICP Vegetation programme) in Southeastern Europe and is widely distributed in the region. In addition to their biomonitoring role, mosses are applied in some countries as a traditional medicine for the treatment of eczema, cuts, burns, eye diseases, etc. Therefore, the chemical and lipid composition of the moss H. cupressiforme is of interest to establish their possible application in different fields. The chemical composition of the moss was examined regarding total lipids, proteins, carbohydrates (i.e., fibres), ash, and moisture content. The main lipid-soluble bioactive components were determined as sterols, tocopherols, phospholipids and fatty acids. The major fatty acids were linoleic (14.9%), oleic (13.8%), palmitic (12.5%) and α-linolenic (11.3%) acids. Unsaturated fatty acids (56.4%) prevailed in the glyceride oil, in which the polyunsaturated ones constituted 32.5%. The lipid indices (atherogenicity, thrombogenicity, hypocholesterolemic/hypercholesterolemic ratio, peroxidability, and oxidation stability index) were also theoretically calculated based on the fatty acid composition of the moss lipids to establish their health benefits and the rate of oxidation. The primary results of this study revealed H. cupressiforme to be a promising alternative source of bioactive compounds that could be implemented in supplements with health-promoting effects.

Exploring sustainable alternatives: Wood distillate alleviates the impact of bioplastic in basil plants

The growing interest in bioplastics and bio-based crop management products in agriculture is driven by the Sustainable Development Goals of the 2030 Agenda. However, recent research has raised concerns about the sustainability of bioplastics due to their potential negative impact on crop growth and yield, with implications for the environment and human health. In this study, wood distillate (WD) was evaluated as a natural enhancer of plant growth and defence system to mitigate the negative impact of a starch-based bioplastic on basil (Ocimum basilicum L.) plants. The study analyzed physiological and biochemical changes in basil plants subjected for 35 days to single or combined treatments of WD and bioplastic by measuring biomarkers of healthy growth, such as soluble proteins, sugars, vitamin C, and malondialdehyde (MDA). The results showed that WD promoted basil development, whereas the presence of bioplastic hindered it. Interestingly, WD did not affect sugars but increased vitamin C by 12 %, which is considered a positive effect as changes in sugar levels could indicate plant stress. In contrast, bioplastic resulted in reduced sugars (-41 %) and increased (+17 %) MDA level, while vitamin C content remained unchanged. However, when WD was added to plants grown with bioplastic, it elevated the levels of all examined parameters, except for sugars and vitamin C, which experienced reductions (-66 % and 33 %, respectively). Intriguingly, despite this reduction, the observed direct correlation between sugar and vitamin C contents was maintained, indicating that the decrease in sugar content may have reached a critical threshold. This study suggests that the use of WD has the potential to alleviate the adverse effects of bioplastic on basil growth and development and highlights the importance of adopting sustainable practices in agriculture, as well as the need for a critical assessment of the environmental impact of new technologies and products.

Green leaf proteins: a sustainable source of edible plant-based proteins

The rise in the global population, which is projected to reach 9.7 billion by 2050, has resulted in an increased demand for proteins in the human diet. The green leaves of many plants are an affordable, abundant, and sustainable source of proteins suitable for human consumption. This article reviews the various sources of green leaf proteins that may play an important role in alleviating global malnutrition, including those from alfalfa, amaranth, cabbage, cassava, duckweed, moringa, olive, radish, spinach, sugar beet, and tea. The structure of green leaves and the location of the proteins within these leaves are described, as well as methods for extracting and purifying these proteins. The composition, nutritional profile, and functional attributes of green leaf proteins are then discussed. The potential advantages and disadvantages of using green leaf proteins as functional food ingredients are highlighted. The importance of obtaining a better understanding of the composition and structure of different green leaves and the proteins extracted from them is highlighted. This includes an assessment of non-protein nitrogen and anti-nutritional compounds that may be present. Furthermore, the impact of isolation and purification techniques on the functionality of the plant protein ingredients obtained must be carefully evaluated.

Applications of Enzyme Technology to Enhance Transition to Plant Proteins: A Review

As the plant-based food market grows, demand for plant protein is also increasing. Proteins are a major component in foods and are key to developing desired structures and textures. Seed storage proteins are the main plant proteins in the human diet. They are abundant in, for example, legumes or defatted oilseeds, which makes them an excellent candidate to use in the development of novel plant-based foods. However, they often have low and inflexible functionalities, as in nature they are designed to remain densely packed and inert within cell walls until they are needed during germination. Enzymes are often used by the food industry, for example, in the production of cheese or beer, to modify ingredient properties. Although they currently have limited applications in plant proteins, interest in the area is exponentially increasing. The present review first considers the current state and potential of enzyme utilization related to plant proteins, including uses in protein extraction and post-extraction modifications. Then, relevant opportunities and challenges are critically discussed. The main challenges relate to the knowledge gap, the high cost of enzymes, and the complexity of plant proteins as substrates. The overall aim of this review is to increase awareness, highlight challenges, and explore ways to address them.

Green Chemistry to Modify Functional Properties of Crambe Protein Isolate-Based Thermally Formed Films

Proteins are promising precursors to be used in production of sustainable materials with properties resembling plastics, although protein modification or functionalization is often required to obtain suitable product characteristics. Here, effects of protein modification were evaluated by crosslinking behavior using high-performance liquid chromatography (HPLC), secondary structure using infrared spectroscopy (IR), liquid imbibition and uptake, and tensile properties of six crambe protein isolates modified in solution before thermal pressing. The results showed that a basic pH (10), especially when combined with the commonly used, although moderately toxic, crosslinking agent glutaraldehyde (GA), resulted in a decrease in crosslinking in unpressed samples, as compared to acidic pH (4) samples. After pressing, a more crosslinked protein matrix with an increase in β-sheets was obtained in basic samples compared to acidic samples, mainly due to the formation of disulfide bonds, which led to an increase in tensile strength, and liquid uptake with less material resolved. A treatment of pH 10 + GA, combined either with a heat or citric acid treatment, did not increase crosslinking or improve the properties in pressed samples, as compared to pH 4 samples. Fenton treatment at pH 7.5 resulted in a similar amount of crosslinking as the pH 10 + GA treatment, although with a higher degree of peptide/irreversible bonds. The strong bond formation resulted in lack of opportunities to disintegrate the protein network by all extraction solutions tested (even for 6 M urea + 1% sodium dodecyl sulfate + 1% dithiothreitol). Thus, the highest crosslinking and best properties of the material produced from crambe protein isolates were obtained by pH 10 + GA and pH 7.5 + Fenton, where Fenton is a greener and more sustainable solution than GA. Therefore, chemical modification of crambe protein isolates is effecting both sustainability and crosslinking behavior, which might have an effect on product suitability.

Physicochemical Characteristics and Microstructure of Ancient and Common Wheat Grains Cultivated in Romania

Different wheat species, common wheat (Triticum aestivum subsp. aestivum), spelt (Triticum aestivum subsp. spelta) and einkorn (Triticum monococcum subsp. monococcum), were analyzed for physicochemical (moisture, ash, protein, wet gluten, lipid, starch, carbohydrates, test weight and thousand-kernel mass) and mineral elements (Ca, Mg, K, Na, Zn, Fe, Mn and Cu) concentrations in grains. Additionally, wheat grain microstructure was determined using a scanning electron microscope. SEM micrographs of wheat grains show that einkorn has smaller type A starch granule diameters and more compact protein bonds compared to common wheat and spelt grains, making it easier to digest. The ancient wheat grains presented higher values for ash, protein, wet gluten and lipid content compared to the common wheat grains, whereas the carbohydrates and starch content were significantly (p < 0.05) lower. The mean values showed that spelt (Triticum aestivum subsp. spelta) grains presented the highest values for Ca, Mg and K, while einkorn (Triticum monococcum subsp. monococcum) grains had the highest values for the microelements Zn, Mn and Cu. The highest values of Fe were recorded for common wheat varieties whereas no significant differences among the species were obtained for Na content. The principal component analysis (p > 0.05) between wheat flours characteristics showed a close association between wheat grain species and between the chemical characteristics of gluten and protein content (r = 0.994), lipid and ash content (r = 0.952) and starch and carbohydrate content (r = 0.927), for which high positive significant correlations (p < 0.05) were obtained. Taking into account that Romania is the fourth largest wheat producer at the European level, this study is of great global importance. According to the results obtained, the ancient species have higher nutritional value from the point of view of chemical compounds and macro elements of minerals. This may be of great importance for consumers who demand bakery products with high nutritional quality.

Molecular dynamics simulation of thermal characteristics of globulin protein dissolved in dilute salt solutions using equilibrium and non-equilibrium methods

The aggregation of 7S globulin protein (7SGP) in mature soybean (Glycine max) seeds is an extracellular matrix protein. This atomic compound can be detected in various food products. So, this protein structure's thermal properties (TP) can be important for various food industry products. Molecular Dynamics (MD) simulations describe the atomic arrangement of this protein and forecast TP of them in various initial conditions. The present computational work estimates the 7SGP thermal behavior (TB) by equilibrium (E) and non-equilibrium (NE) methods. In these two methods, the 7SGP is represented using DREIDING interatomic potential. MD outputs predicted 0.59 and 0.58 W/mK values for thermal conductivity (TC) of 7SGP at T₀ = 300 K and P₀ = 1 bar using E and NE methods. Furthermore, computational results represented that the pressure (P) and temperature (T) are significant factors for the TB of 7SGP. Numerically, TC of 7SGP reaches 0.68 W/mK, 0.52 W/mK by T/P increasing. MD results predicted the interaction energy (IE) between 7SGP and aqueous media could fluctuate between -110.64 and 161.53 kcal/mol by the change in T/P after t = 10 ns?These results should be supposed to design new methods for various food industry purposes, such as producing and processing edible oils.

Changes in Serum Protein-Peptide Patterns in Atopic Children Allergic to Plant Storage Proteins

Next to cow's milk and eggs, plant foods, i.e., legumes, tree nuts and cereal grains, most often sensitise atopic children. Storage proteins constitutes the most relevant protein fraction of plant foods, causing primary sensitisation. They exhibit strong allergenic properties and immunogenicity. Our goal was to analyse sensitisation to 26 plant storage proteins in a group of 76 children aged 0-5 years with chronic symptoms of atopic dermatitis using Allergy Explorer ALEX2 and to discover changes in serum protein-peptide patterns in allergic patients with the use of MALDI-TOF-MS. We reported that 25% of children were allergic to 2S albumins, 19.7% to 7S globulins, 13.2% to 11S globulins and 1.3% to cereal prolamins. The most common allergenic molecules were Ara h 1 (18.4%), Ara h 2 (17.1%), Ara h 6 (15.8%) and Ara h 3 (11.8%) from peanuts, and the mean serum sIgE concentrations in allergic patients were 10.93 kUA/L, 15.353 kUA/L, 15.359 kUA/L and 9.038 kUA/L, respectively. In children allergic to storage proteins compared to the other patients (both allergic and non-allergic), the cell cycle control protein 50A, testis-expressed sequence 13B, DENN domain-containing protein 5A and SKI family transcriptional corepressor 2 were altered. Our results indicate that the IgE-mediated allergy to storage proteins is a huge problem in a group of young, atopic children, and show the potential of proteomic analysis in the prediction of primary sensitisation to plant foods. It is the next crucial step for understanding the molecular consequences of allergy to storage proteins.

Natural carriers: Recent advances in their use to improve the stability and bioaccessibility of food active compounds

In the last decades, the incorporation of bioactive compounds in food supplements aroused the attention of scientists. However, these ingredients often exhibit both low solubility and stability and their poor bioaccessibility within the gastrointestinal tract limits their effectiveness. To overcome these drawbacks, many carriers have been investigated for encapsulating nutraceuticals and enhancing their bioavailability. It is note that several different vegetable wall materials have been applied to build delivery systems. Considering their encapsulation mechanism, lipid and protein-based carriers display specific interaction patterns with bioactives, whereas polysaccharidic-based carriers can entrap them by creating porous highly stable networks. To maximize the encapsulation efficiency, mixed systems are very promising. Following the current goal of using natural and sustainable ingredients, only a limited number of studies about the isolation of new ingredients from agro-food waste are available. In this review, a comprehensive overview of the state of art in the development of innovative natural lipid-, protein- and polysaccharide-based plant carriers is presented, focusing on their application as food active compounds. Different aspects to be considered in the design of delivery systems are discussed, including the carrier structure and chemical features, the interaction between the encapsulating and the core material, and the parameters affecting bioactives entrapment.

Comparison of grain protein profiles of Brazilian cowpea (Vigna unguiculata) cultivars based on principal component analysis

This study aims to compare the grain protein profile of four Brazilian cowpea cultivars (BRS Aracê, BRS Itaim, BRS Pajeú, and BRS Xiquexique) by two-dimensional electrophoresis (2-DE) and principal component analysis (PCA). 2-DE efficiently separate cowpea protein profiles, showing high homogeneity among the four cultivars. In addition, the principal component analysis indicated that there is a difference in abundance of proteins among the cultivars. The cultivars BRS Aracê and BRS Xiquexique, both biofortified in iron and zinc, were separated from the cultivars BRS Itaim and BRS Pajeú. These results demonstrate that protein profiles can be used to discriminate cowpea varieties.

Graphical Abstract

Amino acid composition, mineral profile, free radical scavenging ability, and carbohydrase inhibitory properties of Moringa oleifera seed globulin, hydrolysates, and membrane fractions

The nutritional-amino acid profile and mineral element of Moringa oleifera seed globulin (GLO) and its hydrolysates as well as the in vitro bioactive properties-antioxidant, alpha-amylase, and alpha-glucosidase inhibition of the GLO, hydrolysates, and membrane fractions were reported. The results showed that M. oleifera contained significant amounts of essential amino acids (EAA), which are more than the minimum required by the Food and Agricultural Organization for children, except for tryptophan, which was the limiting amino acid. However, hydrolysis mostly led to a reduction in the contents of the EAA. While the process of hydrolysis and the subsequent membrane fractionation produced peptides with improved activities in 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulphonic acid radical scavenging ability and oxygen radical absorbance capacity, this process produced no activities in superoxide radical scavenging ability, α-amylase, and α-glucosidase inhibitory potentials of some of the hydrolysates and peptides fractions. In summary, M. oleifera seed peptide fraction (<3 kDa) from the alcalase-derived hydrolysate contains potent antioxidants but relatively low in vitro antidiabetic properties. PRACTICAL APPLICATIONS: Several studies have established the ability of proteins, including hydrolysate and peptide fractions to provide some bioactive properties such as antioxidant, antidiabetic, anti-inflammatory among others. However, because protein functionalities are influenced by several factors such as the source, type, processing method employed among others, research has continued to evaluate the bioactivities of proteins under different conditions. In this study, therefore, we reported the impact of processing methods (hydrolysis, enzyme type, and peptide size) on the nutritional, antioxidant, and in vitro antidiabetic properties of M. oleifera seed globulin, its hydrolysates, and membrane fractions. This information plays an important role in the further exploitation of M. oleifera seed proteins in the development of functional foods and nutraceuticals.

Identification and analysis of proline-rich proteins and hybrid proline-rich proteins super family genes from Sorghum bicolor and their expression patterns to abiotic stress and zinc stimuli

Systematic genome-wide analysis of Sorghum bicolor revealed the identification of a total of 48 homologous genes comprising 21 proline-rich proteins (PRPs) and 27 hybrid proline-rich proteins (HyPRPs). Comprehensive scrutiny of these gene homologs was conducted for gene structure, phylogenetic investigations, chromosome mapping, and subcellular localization of proteins. Promoter analysis uncovered the regions rich with phosphorous- (BIHD), ammonium-, sulfur-responsive (SURE), and iron starvation-responsive (IRO2) along with biotic, abiotic, and development-specific cis-elements. Further, PRPs exhibit more methylation and acetylation sites in comparison with HyPRPs. miRNAs have been predicted which might play a role in cleavage and translation inhibition. Several of the SbPRP genes were stimulated in a tissue-specific manner under drought, salt, heat, and cold stresses. Additionally, exposure of plants to abscisic acid (ABA) and zinc (Zn) also triggered PRP genes in a tissue-dependent way. Among them, SbPRP17 has been found upregulated markedly in all tissues irrespective of the stress imposed. The expressions of SbHyPRPs, especially SbHyPRP2, SbHyPRP6, and SbHyPRP17 were activated under all stresses in all three tissues. On the other hand, SbHyPRP8 (root only) and SbHyPRP12 (all three tissues) were highly responsive to cold stress and ABA while SbHyPRP26 was induced by drought and Zn in the stem. Taken together, this study indicates the critical roles that SbPRPs and SbHyPRPs play during diverse abiotic stress conditions and notably the plausible roles that these genes play upon exposure to zinc, the crucial micronutrient in plants.

Genome-wide identification and multiple abiotic stress transcript profiling of potassium transport gene homologs in Sorghum bicolor

Potassium (K⁺) is the most abundant cation that plays a crucial role in various cellular processes in plants. Plants have developed an efficient mechanism for the acquisition of K⁺ when grown in K⁺ deficient or saline soils. A total of 47 K⁺ transport gene homologs (27 HAKs, 4 HKTs, 2 KEAs, 9 AKTs, 2 KATs, 2 TPCs, and 1 VDPC) have been identified in Sorghum bicolor. Of 47 homologs, 33 were identified as K⁺ transporters and the remaining 14 as K⁺ channels. Chromosome 2 has been found as the hotspot of K⁺ transporters with 9 genes. Phylogenetic analysis revealed the conservation of sorghum K⁺ transport genes akin to Oryza sativa. Analysis of regulatory elements indicates the key roles that K⁺ transport genes play under different biotic and abiotic stress conditions. Digital expression data of different developmental stages disclosed that expressions were higher in milk, flowering, and tillering stages. Expression levels of the genes SbHAK27 and SbKEA2 were higher during milk, SbHAK17, SbHAK11, SbHAK18, and SbHAK7 during flowering, SbHAK18, SbHAK10, and 23 other gene expressions were elevated during tillering inferring the important role that K⁺ transport genes play during plant growth and development. Differential transcript expression was observed in different tissues like root, stem, and leaf under abiotic stresses such as salt, drought, heat, and cold stresses. Collectively, the in-depth genome-wide analysis and differential transcript profiling of K⁺ transport genes elucidate their role in ion homeostasis and stress tolerance mechanisms.

Proteomic and computational characterisation of 11S globulins from grape seed flour by-product and its interaction with malvidin 3-glucoside by molecular docking

Grape seed flour by-product (GSBP) is an economic and renewable source of proteins, increasingly being explored due to interesting technological application such as colour protection in rich-anthocyanins beverages. Globulin-like proteins from GSBP were characterised by proteomic and computational studies. MALDI TOF/TOF analysis revealed the presence of two 11S globulins (acid and basic), whose 3D structures have been elucidated for the first time in Vitis vinifera L. grape seeds by using homology models and molecular dynamics. The secondary structure showed 11 α-helices and 25 β-sheets for acid and 12 α-helices and 24 β-sheets for basic 11S globulins. Molecular docking results indicate that both grape seed 11S globulins could establish different types of non-covalent interactions (π-π) with malvidin 3-O-glucoside (wine anthocyanin), which suggest a possible colour protection similar to that occurring in copigmentation phenomenon. These findings provide valuable information of globulin family proteins that could be relevant in food industry applications.

How can the analysis of reserve dynamics after fire support the phenological insight of Bulbostylis paradoxa (Spreng.) Lindm (Cyperaceae)?

Carbohydrate reserves are an essential key to plant survival from disturbance. Therefore, studying the different storage organs and types of reserves makes it possible to understand the dynamics of singular plants such as Bulbostylis paradoxa (Spreng.) Lindm, which presents flowering triggered by fire in the Cerrado. Physiological response to fire frequency is detailed by measuring the plant's reserves after a fire disturbance and which carbohydrates are more available for its use. It was measured the concentrations of starch, amino acids, total soluble carbohydrates and soluble proteins in leaves (control), flowers (burning) and caudex of B. paradoxa, in unburned individuals (control), and burned individuals (annually and biennially, obtained 48 h and 15 days after fire). Starch concentrations increased at both fire frequencies in all parts of the plant, as did carbohydrate concentrations. In amino acids, an increase in the concentration of flowers from individuals burned biennially 48 h after fire was observed. The protein concentration showed a decrease in burned plants. Furthermore, the two burning frequencies and the days following the fire can influence the storage of such reserves.

Clustering and cross-linking of the wheat storage protein α-gliadin: A combined experimental and theoretical approach

Our aim was to understand mechanisms for clustering and cross-linking of gliadins, a wheat seed storage protein type, monomeric in native state, but incorporated in network while processed. The mechanisms were studied utilizing spectroscopy and high-performance liquid chromatography on a gliadin-rich fraction, in vitro produced α-gliadins, and synthetic gliadin peptides, and by coarse-grained modelling, Monte Carlo simulations and prediction algorithms. In solution, gliadins with α-helix structures (dip at 205 nm in CD) were primarily present as monomeric molecules and clusters of gliadins (peaks at 650- and 700-s on SE-HPLC). At drying, large polymers (R_g 90.3 nm by DLS) were formed and β-sheets increased (14% by FTIR). Trained algorithms predicted aggregation areas at amino acids 115-140, 150-179, and 250-268, and induction of liquid-liquid phase separation at P- and Poly-Q-sequences (Score = 1). Simulations showed that gliadins formed polymers by tail-to-tail or a hydrophobic core (Kratky plots and R_ee = 35 and 60 for C- and N-terminal). Thus, the N-terminal formed clusters while the C-terminal formed aggregates by disulphide and lanthionine bonds, with favoured hydrophobic clustering of similar/exact peptide sections (synthetic peptide mixtures on SE-HPLC). Mechanisms of clustering and cross-linking of the gliadins presented here, contribute ability to tailor processing results, using these proteins.

Machine learning: its challenges and opportunities in plant system biology

Sequencing technologies are evolving at a rapid pace, enabling the generation of massive amounts of data in multiple dimensions (e.g., genomics, epigenomics, transcriptomic, metabolomics, proteomics, and single-cell omics) in plants. To provide comprehensive insights into the complexity of plant biological systems, it is important to integrate different omics datasets. Although recent advances in computational analytical pipelines have enabled efficient and high-quality exploration and exploitation of single omics data, the integration of multidimensional, heterogenous, and large datasets (i.e., multi-omics) remains a challenge. In this regard, machine learning (ML) offers promising approaches to integrate large datasets and to recognize fine-grained patterns and relationships. Nevertheless, they require rigorous optimizations to process multi-omics-derived datasets. In this review, we discuss the main concepts of machine learning as well as the key challenges and solutions related to the big data derived from plant system biology. We also provide in-depth insight into the principles of data integration using ML, as well as challenges and opportunities in different contexts including multi-omics, single-cell omics, protein function, and protein-protein interaction. KEY POINTS: • The key challenges and solutions related to the big data derived from plant system biology have been highlighted. • Different methods of data integration have been discussed. • Challenges and opportunities of the application of machine learning in plant system biology have been highlighted and discussed.

Genome‑wide identification of CAMTA gene family members in rice (Oryza sativa L.) and in silico study on their versatility in respect to gene expression and promoter structure

The calmodulin-binding transcription activator (CAMTA) is a family of transcriptional factors containing a cluster of calmodulin-binding proteins that can activate gene regulation in response to stresses. The presence of this family of genes has been reported earlier, though, the comprehensive analyses of rice CAMTA (OsCAMTA) genes, their promoter regions, and the proteins were not deliberated till date. The present report revealed the existence of seven CAMTA genes along with their alternate transcripts in five chromosomes of rice (Oryza sativa) genome. Phylogenetic trees classified seven CAMTA genes into three clades indicating the evolutionary conservation in gene structure and their association with other plant species. The in silico study was carried out considering 2 kilobases (kb) promoter regions of seven OsCAMTA genes regarding the distribution of transcription factor binding sites (TFbs) of major and plant-specific transcription factors whereas OsCAMTA7a was identified with highest number of TFbs, while OsCAMTA4 had the lowest. Comparative modelling, i.e., homology modelling, and molecular docking of the CAMTA proteins contributed the thoughtful comprehension of protein 3D structures and protein-protein interaction with probable partners. Gene ontology annotation identified the involvement of the proteins in biological processes, molecular functions, and localization in cellular components. Differential gene expression study gave an insight on functional multiplicity to showcase OsCAMTA3b as most upregulated stress-responsive gene. Summarization of the present findings can be interpreted that OsCAMTA gene duplication, variation in TFbs available in the promoters, and interactions of OsCAMTA proteins with their binding partners might be linked to tolerance against multiple biotic and abiotic cues.

Evaluation of physiological and biochemical responses of pistachio plants (Pistacia vera L.) exposed to pesticides

Pesticides may manipulate plant physiology as non-target organisms. In this study, we examined biochemical responses of pistachio plants (Pistacia vera L.) to imidacloprid and phosalone as common pesticides used to control pistachio psyllids. Enzymatic characterization in treated plants with pesticides showed greater specific activities of superoxide dismutase, catalase, ascorbate peroxidase, guaiacol peroxidase, phenylalanine ammonia-lyase, glutathione reductase, and glutathione S-transferase compared with untreated plants during 14 days after treatment. Further experiments displayed elevated levels of total phenols and total proteins coupled with significant increases in proline and total soluble carbohydrate contents in treated plants in comparison to untreated plants. Moreover, pesticide treatment leads to a significant decrease in polyphenol oxidase activity. Nevertheless, no significant changes in contents of hydrogen peroxide, malondialdehyde, total chlorophyll, and electrolyte leakage index were obtained in treated plants. Pesticides' impacts on host plant physiology resulted in similar responses between two pesticides with differences in peak days. Overall, the findings of this study provide an insight into the side effects of phosalone and imidacloprid, chemicals with no specific target site in plants, on the physiology and biochemistry of pistachio plants at recommended rates.

Physicochemical characterisation of kafirins extracted from sorghum grain and dried distillers grain with solubles related to their biomaterial functionality

Kafirin, the hydrophobic prolamin storage protein in sorghum grain is enriched when the grain is used for bioethanol production to give dried distillers grain with solubles (DGGS) as a by-product. There is great interest in DDGS kafirin as a new source for biomaterials. There is however a lack of fundamental understanding of how the physicochemical properties of DDGS kafirin having been exposed to the high temperature conditions during ethanol production, compare to kafirin made directly from the grain. An understanding of these properties is required to catalyse the utilisation of DDGS kafirin for biomaterial applications. The aim of this study was to extract kafirin directly from sorghum grain and from DDGS derived from the same grain and, then perform a comparative investigation of the physicochemical properties of these kafirins in terms of: polypeptide profile by sodium-dodecyl sulphate polyacrylamide gel electrophoresis; secondary structure by Fourier transform infra-red spectroscopy and x-ray diffraction, self-assembly behaviour by small-angle x-ray scattering, surface morphology by scanning electron microscopy and surface chemical properties by energy dispersive x-ray spectroscopy. DDGS kafirin was found to have very similar polypeptide profile as grain kafirin but contained altered secondary structure with increased levels of β-sheets. The structure morphology showed surface fractals and surface elemental composition suggesting enhanced reactivity with possibility to endow interfacial wettability. These properties of DDGS kafirin may provide it with unique functionality and thus open up opportunities for it to be used as a novel food grade biomaterial.

Components of plant-derived food allergens: Structure, diagnostics, and immunotherapy

A large number of plant-derived food allergen components have been identified to date. Although these allergens are diverse, they often share common structural features such as numerous disulfide bonds or oligomeric structures. Furthermore, some plant-derived food allergen components cross-react with pollen allergens. Since the relationship between allergen components and clinical symptoms has been well characterized, measurements of specific IgE to these components have become useful for the accurate clinical diagnosis and selection of optimal treatment methods for various allergy-related conditions including allergy caused by plant-derived foods. Herein, I have described the types and structures of different plant allergen components and outlined the diagnosis as well as treatment strategies, including those reported recently, for such substances. Furthermore, I have also highlighted the contribution of allergen components to this field.

Evaluating the Endophytic Activities of Beauveria bassiana on the Physiology, Growth, and Antioxidant Activities of Extracts of Lettuce (Lactuca sativa L.)

Endophytic entomopathogens have growth promoting, nutrient fortifying, and anti-insect properties that could improve the yield and quality of lettuce (Lactuca sativa L.). Lactuca sativa is a vegetable crop with high demand; however, it is susceptible to aphid infestations. This study's objectives were to assess the pathogenicity of Beauveria bassiana (strain: SM3) (Bals.) Vuil. (Hypocreales) against Myzus persicae Sulzer, tissue colonization of lettuce by conidia of B. bassiana, as well as the effects of fungal inoculation on growth, tissue nutrient content, and proximate composition of the lettuce plants. Furthermore, the involvement of tissue nutrients in mediating the influence of endophytic fungus on the plant traits was examined. Insects and plants were exposed to four fungal conidial concentrations: 0, 1 × 10⁶, 1 × 10⁷ and 1 × 10⁸ conidia mL^-1 in an anti-insect bioassay and a greenhouse experiment, respectively. The B. bassiana strain was pathogenic against M. persicae, inducing mean insect mortality of 78% at the highest concentration (1 × 10⁸ conidia mL^-1). The B. bassiana endophytically colonized up to 76% of plants exposed to 1 × 10⁸ conidia mL^-1. Crown size and plant height varied significantly among treatments. However, the plant fresh and dry weights and nutrient elements N, P, K, Ca, and Mg did not vary significantly among treatments. Among the plant macronutrients assessed, only tissue carbon content was significantly (p < 0.01) affected by conidial treatments. The tissue C and Cu contents significantly correlated with the antioxidant capacity of the lettuce plants. Most of the micronutrients, viz. Mn, Fe, Cu, and B were remarkably higher (p < 0.05) in the fungus-treated plants than in the control plants. The antioxidant capacity (FRAP and TEAC) of plant extracts varied significantly (p < 0.001) among treatments, with the highest conidial treatment yielding the most increased antioxidant activity. In conclusion, the B. bassiana strain was endophytic to lettuce, pathogenic against M. persicae, and induced increased micro-nutrient tissue contents and antioxidant activities. This study demonstrated that B. bassiana could be potentially used in the biofortification of nutritive and medicinal qualities of plants.

Methods for the Modification and Evaluation of Cereal Proteins for the Substitution of Wheat Gluten in Dough Systems

The substitution of wheat gluten in the food industry is a relevant research area because the only known treatment for celiac disease is abstinence from this protein complex. The use of gluten-free cereals in dough systems has demonstrated that the viscoelastic properties of gluten cannot be achieved without the modification of the protein fraction. The quality of the final product is determined by the ability of the modification to form a matrix similar to that of gluten and to reach this, different methods have been proposed and tested. These procedures can be classified into four main types: chemical, enzymatic, physical, and genetic. This article provides a comprehensive review of the most recent research done in protein modification of cereal and pseudocereals for gluten substitution. The reported effects and methodologies for studying the changes made with each type of modification are described; also, some opportunity areas for future works regarding the study of the effect of protein modifications on gluten-free products are presented.

Glutenin and Gliadin, a Piece in the Puzzle of their Structural Properties in the Cell Described through Monte Carlo Simulations

Gluten protein crosslinking is a predetermined process where specific intra- and intermolecular disulfide bonds differ depending on the protein and cysteine motif. In this article, all-atom Monte Carlo simulations were used to understand the formation of disulfide bonds in gliadins and low molecular weight glutenin subunits (LMW-GS). The two intrinsically disordered proteins appeared to contain mostly turns and loops and showed "self-avoiding walk" behavior in water. Cysteine residues involved in intramolecular disulfide bonds were located next to hydrophobic peptide sections in the primary sequence. Hydrophobicity of neighboring peptide sections, synthesis chronology, and amino acid chain flexibility were identified as important factors in securing the specificity of intramolecular disulfide bonds formed directly after synthesis. The two LMW-GS cysteine residues that form intermolecular disulfide bonds were positioned next to peptide sections of lower hydrophobicity, and these cysteine residues are more exposed to the cytosolic conditions, which influence the crosslinking behavior. In addition, coarse-grained Monte Carlo simulations revealed that the protein folding is independent of ionic strength. The potential molecular behavior associated with disulfide bonds, as reported here, increases the biological understanding of seed storage protein function and provides opportunities to tailor their functional properties for different applications.