Accurate protein solubility prediction is crucial in screening suitable candidates for food application. Existing models often rely only on sequences, overlooking important structural details. In this study, a regression model for protein solubility was developed using both the sequences and predicted structures of 2983 E. coli proteins. The sequence and structural level properties of the proteins were bioinformatically extracted and subjected to multilayer perceptron (MLP). Moreover, residue level features and contact maps were utilized to construct a graph convolutional network (GCN). The out-of-fold predictions of the two models were combined and fed into multiple meta-regressors to create a stacking model. The stacking model with support vector regressor (SVR) achieved R2 of 0.502 and 0.468 on test and external validation datasets, respectively, displaying higher performance compared to existing regression models. Based on the improved performance compared to its based models, the stacking model effectively captured the strength of its base models as well as the significance of the different features used. Furthermore, the model\'s transferability was indirectly validated on a dataset of seed storage proteins using Osborne definition as well as on a case study using molecular dynamic simulation, showing potential for application beyond microbial proteins to food and agriculture-related ones.

Plant-based proteins offer sustainable and nutritious alternatives to animal proteins with their techno-functional attributes influencing product quality and designer food development. Due to the inherent complexities of plant proteins, proper extraction and modifications are vital for their effective utilization. This review highlights the emerging sources of plant-based proteins, and the recent statistics of the techniques employed for pretreatment, extraction, and modifications. The pretreatment, extraction and modification approach to modify plant proteins have been classified, addressed, and the recent applications of such methodologies are duly indicated. Furthermore, this study furnishes novel perspectives regarding the potential impacts of emerging technologies on the intricate dynamics of plant proteins. A thorough review of 100 articles (2018-2024) shows the researchers\' keen interest in investigating novel plant proteins and how they can be used; seeds being the main source for protein extraction, followed by legumes. Use of by-products as a protein source is increasing rapidly, which is noteworthy. Protein studies still lack knowledge on protein fraction, antinutrients, and pretreatments. The use of physical methods and their combination with other techniques are increasing for effective and environmentally friendly extraction and modification of plant proteins. Several studies explore the effect of protein changes on their function and nutrition, especially with a goal of replacing ingredients with plant proteins that have improved or enhanced qualities. However, the next step is to investigate the sophisticated modification methods for deeper insights into food safety and toxicity.

Lupin species provide essential nutrients and bioactive compounds. Within pulses, they have one of the highest contents of proteins and fibers and are among the poorest in carbohydrates. The Mediterranean region is an important cradle area of the origin and domestication of cultivated white lupin (Lupinus albus L.). In this work, we present the characterization of 19 white lupin landraces collected from several sites in southern Italy, characterized by different pedoclimatic conditions. The protein contents and electrophoretic patterns, total polyphenols, phytic acid, lipids and phosphorous content, and reducing and anti-tryptic activities have been determined for each landrace. The relationships of the compositional characteristics, the area of origin of landraces and between compositional characteristics and thermo-pluviometric trends that occurred in the genotype comparison field during the two-year period between 2019 and 2020 are compared and discussed. From a nutritional point of view, some of the analyzed landraces differ from the commercial reference. The panel of molecular analyses performed can help in building an identity card for the grain to rapidly identify those varieties with the desired characteristics.

Blackberry fruit contains high levels of nutrients and phenolic compounds. Blackberry pomace accounts for 20~30% of its whole fruit during processing and is generally treated as fertilizer. Blackberry pomace has many seeds that contain carbohydrates, polyphenols, flavonoids, pectin, protein, and other bioactive nutrients. However, its functional properties and seed protein compositions have not been reported. We used a single-factor experiment, response surface, and Osborne isolate method to extract protein isolate, albumin, globulin, glutelin, and prolamin from blackberry seeds for the first time and evaluated their characteristics and functional properties. Glutelin and protein isolate showed good water-holding capacity, emulsification, and foaming capacity, while albumin and globulin showed good oil-holding capacity and thermal stability. They were found to have good antioxidant activities that might be good DPPH free radical scavengers, especially prolamin, which has the lowest IC50 value (15.76 μg/mL). Moreover, globulin had the lowest IC50 value of 5.03 μg/mL against Hela cells, 31.82 μg/mL against HepG2 cells, and 77.81 μg/mL against MCF-7 cells and a high selectivity index (SI), which suggested globulin had better anti-cervical, antihepatoma, and anti-breast activity but relatively low cytotoxicity. These seed proteins may have great prospects for the development and application of food and drugs in the future.

Improving the proteins and amino acid contents of rice seeds is one of the prime objectives of plant breeders. We recently developed an EMS mutant/high-protein mutant (HPM) of rice that exhibits 14.8% of the total protein content as compared to its parent Dharial (wild-type), which shows only 9.3% protein content in their mature seeds. However, the mechanisms underlying the higher protein accumulation in these HPM seeds remain largely elusive. Here, we utilized high-throughput proteomics to examine the differences in the proteome profiles of the embryo, endosperm, and bran tissues of Dharial and HPM seeds. Utilizing a label-free quantitative proteomic and subsequent functional analyses of the identified proteins revealed that nitrogen compound biosynthesis, intracellular transport, protein/amino acid synthesis, and photosynthesis-related proteins were specifically enriched in the endosperm and bran of the high-protein mutant seed. Our data have uncovered proteome-wide changes highlighting various functions of metabolic pathways associated with protein accumulation in rice seeds.

The presence of so-called anti-nutritional factors can reduce the bioavailability of nutrients following consumption of seeds which are otherwise an excellent source of proteins, carbohydrates and micronutrients. Among the proteins associated with negative effects on quality in pea (Pisum sativum L.) seeds are lectin, pea albumin 2 (PA2) and trypsin inhibitors (TI). Here we have investigated the impact of these proteins on protein digestibility and amino acid availability, using naturally occurring and derived mutant lines of pea lacking these proteins. The mutations were stacked to generate a triple mutant which was compared with a wild-type progenitor and a line lacking the major seed trypsin inhibitors alone. In vitro digestions following the INFOGEST protocol revealed significant differences in the degree of hydrolysis, protein profile and apparent amino acid availability among the pea variants. Proteins resistant to digestion were identified by MALDI-TOF mass spectrometry and amino acid profiles of digested samples determined. The results indicate that pea seeds lacking certain proteins can be used in the development of novel foods which have improved protein digestibility, and without negative impact on seed protein concentration or yield.

BACKGROUND: The narrow genetic diversity of chickpea is a serious impediment to modern cultivar creation. Seed storage proteins (SSPs) are stable and have minimal or no degradation when subjected to isolation and SDS-PAGE.
RESULTS: We have characterized SSPs of 436 chickpea genotypes, belonging to nine annual Cicer species, originated from 47 countries by SDS-PAGE and determined the extent of genetic diversity in chickpea through clustering. Based on scoring, a total of 44 bands (10 to 170 kDa) were identified, which were all polymorphic. The least appeared protein bands were 11, 160 and 170 kDa where band of 11 and 160 kDa was present exclusively in wild type. Five bands were present in < 10% of genotypes. Bands appeared in 200-300 genotypes were suggested less polymorphic, on contrary bands present in 10-150 genotypes were suggested more polymorphic. Polymorphism of protein bands in context to their potential functions reported in literature were explored and suggested that the glubulins were most and glutelins were least abundant, whereas albumins with their known role in stress tolerance can be used as marker in chickpea breeding. Cluster analysis produced 14 clusters, interestingly three clusters contained only Pakistani genotypes and thus Pakistani genotypes appeared as a separate entity from the rest of the genotypes.
CONCLUSIONS: Our results indicate that SDS-PAGE of SSPs is a powerful technique in determining the genetic diversity plus it is easily adaptable, due to its cost effectiveness in comparison to other genomics tools.

BACKGROUND: The state of Manipur, North East India has distinct topology of hill and valley regions with vast agroclimatic variability, being considered as one of the centers of rice diversity. The indigenous Manipur black rice cultivars exhibit wide range of diversity in morphology, pericarp color, shape and size of grain, aroma, glutinous or non-glutinous features but remain less characterised. Many of these cultivars, such as those named Chakhao, are endowed with multiple health benefits due to high anthocyanins, and hold special importance for the local people. It is important to analyse the genetic diversity and population structure for this germplasm with unique allelic combinations to utilize in rice breeding programme.
RESULTS: We characterized total soluble seed protein fractions to not only fingerprint the 45 indigenous black rice cultivars but assess their genetic relatedness. Cluster analyses generated mainly two groups, complemented by PCoA scatter plot ascertaining geographical distinction. The hill black rice were more diverse. The population structure analysis revealed seven subpopulations indicating high genetic variability. The 24 polymorphic bands were scored in the range of 127.8 to 10.3 kDa comprised of four protein fractions. Three polypeptide bands each were ascribed to known fractions of glutelins and prolamins, while one band each could be described for albumin and globulin fractions, besides other diagnostic bands.
CONCLUSIONS: Some diverse cultivars were Amubi, Chedo Anal, Chipi Buh, Athebu, Poireton, BuPu Mui, Kotha Chahao II. These cultivars can be used in future black rice breeding programmes. This can further prevent genetic erosion and protect intellectual property rights.

L: operculata is a plant commonly found in the North and Northeast of Brazil. Although the regional population knows its medicinal potential, there are few scientific studies about its antimicrobial potential. Thus, this study aimed to characterize the proteins from L. operculata seeds extracted using different solutions and evaluate their antimicrobial potentials. The protein extracts obtained with NaCl and sodium acetate buffer presented the best inhibitory activities against Candida albicans and C. krusei. The study of the mechanism of action revealed proteins from L. operculata seeds induced pore formation on the membrane and ROS overaccumulation. Scanning Electron Microscopy images also showed severe morphological changes in Candida albicans and C. krusei. Proteins from L.operculata seeds did not show antibacterial activity. The enzymatic assays revealed the presence of proteolytic enzymes, serine and cysteine protease inhibitors, and chitinases in both protein extracts. Proteomic analysis by LC-ESI-MS/MS identified 57 proteins related to many biological processes, such as defense to (a)biotic stress, energetic metabolism, protein folding, and nucleotide metabolism. In conclusion, the L. operculata seed proteins have biotechnological potential against the human pathogenic yeasts Candida albicans and C. krusei.

A Bowman-Birk protease, i.e., Mucuna pruriens trypsin inhibitor (MPTI), was purified from the seeds by 55.702-fold and revealed a single trypsin inhibitor on a zymogram with a specific activity of 202.31 TIU/mg of protein. On sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) under non-reducing conditions, the protease trypsin inhibitor fraction [i.e., trypsin inhibitor non-reducing (TINR)] exhibited molecular weights of 74 and 37 kDa, and under reducing conditions [i.e., trypsin inhibitor reducing (TIR)], 37 and 18 kDa. TINR-37 revealed protease inhibitor activity on native PAGE and 37 and 18 kDa protein bands on SDS-PAGE. TINR-74 showed peaks corresponding to 18.695, 37.39, 56.085, and 74.78 kDa on ultra-performance liquid chromatography (UPLC) coupled with electrospray ionization/quadrupole time-of-flight-mass spectrometry (ESI/QTOF-MS). Similarly, TINR-37 displayed 18.695 and 37.39 kDa peaks. Furthermore, TIR-37 and TIR-18 exhibited peaks corresponding to 37.39 and 18.695 kDa. Multiple peaks observed by the UPLC-ESI/QTOF analysis revealed the multimeric association, confirming the characteristic and functional features of Bowman-Birk inhibitors (BBIs). The multimeric association helps to achieve more stability, thus enhancing their functional efficiency. MPTI was found to be a competitive inhibitor which again suggested that it belongs to the BBI family of inhibitors, displayed an inhibitor constant of 1.3 × 10-6 M, and further demonstrates potent anti-inflammatory activity. The study provided a comprehensive basis for the identification of multimeric associates and their therapeutic potential, which could elaborate the stability and functional efficiency of the MPTI in the native state from M. pruriens.