Protein Functionality Research Articles

Rapid and Efficient Isolation of Total RNA-Bound Proteomes by Liquid Emulsion-Assisted Purification of RNA-Bound Protein (LEAP-RBP).

The critical roles of RNA-binding proteins (RBPs) in all aspects of RNA biology fostered the development of methods utilizing ultraviolet (UV) crosslinking and method-specific RNA enrichment steps for proteome-wide identification and assessment of RBP function. Despite the substantial contributions of these UV-based RNA-centric methods to our understanding of RNA-protein interaction networks, their utility is constrained by biases in RBP recovery and significant noise contributions, which can confound meaningful interpretation. To overcome these issues, we recently developed a method termed Liquid Emulsion-Assisted Purification of RNA-Bound Protein (LEAP-RBP) and introduced quantitative signal-to-noise (S:N)-based metrics for the proteome-wide identification of RNA interactomes and accurate assessment of global RBP occupancy dynamics. Compared to existing methodologies, LEAP-RBP provides significant advantages in speed, cost, efficiency, and selectivity for RNA-bound proteins. In this work, we provide a step-by-step guide for the successful application of the LEAP-RBP method for both small- and large-scale investigations of RNA-bound proteomes. Key features • Unbiased and efficient isolation of total RNA-bound protein, RNA, and protein from biological samples. • Cost-effective identification of proteome-wide RNA interactomes and validation of direct RNA-binding protein functionality. • Robust and accurate assessment of context- and/or condition-dependent RBP occupancy state dynamics.

Enhancing Meat Product Quality: Exploring the Effects of Additives on Myofibrillar Protein Functionality

Enhancing Meat Product Quality: Exploring the Effects of Additives on Myofibrillar Protein Functionality

Ingredient Functionality of Soy, Chickpea, and Pea Protein before and after Dry Heat Pretreatment and Low Moisture Extrusion.

This study investigates the impact of dry heat pretreatment on the functionality of soy, chickpea, and pea protein ingredients for use in texturized vegetable protein (TVP) production via low moisture extrusion. The protein powders were heat-treated at temperatures ranging from 80 °C to 160 °C to modulate the extent of protein denaturation and assess their effects on RVA pasting behavior, water absorption capacity (WAC), and color attributes. The results indicate that the pretreatment temperature significantly influenced the proteins' functional properties, with an optimal temperature of 120 °C enhancing pasting properties and maintaining WAC, while a higher pretreatment temperature of 160 °C led to diminished ingredient functionality. Different protein sources exhibited distinct responses to heat pretreatment. The subsequent extrusion processing revealed significant changes in extrudate density and color, with increased density and darkness observed at higher pretreatment temperatures. This research provides insights into the interplay between protein sources, pretreatment conditions, and extrusion outcomes, highlighting the importance of controlled protein denaturation for developing high-quality, plant-based meat analogues. The findings have broad implications for the optimization of meat analogue manufacturing, with the aim of enhancing the sensory experience and sustainability of plant-based foods.

Codon usage bias in yeasts and its correlation with gene expression, growth temperature, and protein structure.

Codon usage bias (CUB) has been described in viruses, prokaryotes, and eukaryotes and has been linked to several cellular and environmental factors, such as the organism's growth temperature, gene expression levels, and regulation of protein synthesis and folding. Most of the studies in this area have been conducted in bacteria and higher eukaryotes, in some cases with different results. In this study, a comparative analysis of CUB in yeasts isolated from cold and template environments was performed in order to evaluate the correlation of CUB with yeast optimal temperature of growth (OTG), gene expression levels, cellular function, and structure of encoded proteins. Among the main findings, highly expressed ORFs tend to have a more similar CUB within and between yeasts, and a direct correlation between codons ending in C and expression level was generally found. A low correspondence between CUB and OTG was observed, with an inverse correlation for some codons ending in C. The clustering of yeasts based on their CUB partially aligns with their OTG, being more consistent for yeasts with lower OTG. In most yeasts, the abundance of preferred codons was generally lower at the 5' end of ORFs, higher in segments encoding beta strand, lower in segments encoding extracellular and transmembrane regions, and higher in "translation" and "energy metabolism" pathways, especially in highly expressed ORFs. Based on our findings, it is suggested that the abundance and distribution of preferred and non-preferred codons along mRNAs contribute to proper protein folding and functionality by regulating protein synthesis rates, becoming a more important factor under conditions that require faster protein synthesis in yeasts.

In-silico screening of missense nsSNPs in Delta-opioid receptor protein and their restoring tendency on MCRT interaction; focusing on dynamic nature

Delta-opioid receptor protein (OPRD1) is one of the potential targets for treating pain. The presently available opioid agonists are known to cause unnecessary side effects. To discover a novel opioid agonist, our research group has synthesized a chimeric peptide MCRT and proved its potential activity through in vivo analysis. Non-synonymous SNPs (nsSNPs) missense mutations affect the functionality and stability of proteins leading to diseases. The current research was focused on understanding the role of MCRT in restoring the binding tendency of OPRD1 nsSNPs missense mutations on dynamic nature in comparison with Deltorphin-II and morphiceptin. The deleterious effects of nsSNPs were analyzed using various bioinformatics tools for predicting structural, functional, and oncogenic influence. The shortlisted nine nsSNPs were predicted for allergic reactions, domain changes, post-translation modification, multiple sequence alignment, secondary structure, molecular dynamic simulation (MDS), and peptide docking influence. Further, the docked complex of three shortlisted deleterious nsSNPs was analyzed using an MDS study, and the highly deleterious shortlisted nsSNP A149T was further analyzed for higher trajectory analysis. MCRT restored the binding tendency influence caused by nsSNPs on the dynamics of stability, functionality, binding affinity, secondary structure, residues connection, motion, and folding of OPRD1 protein.

Methionine sulfoxide reductase B2 protects against cardiac complications in diabetes mellitus

Diabetes mellitus (DM) is a progressive, chronic metabolic disorder characterized by high oxidative stress, which can lead to cardiac damage. Methionine sulfoxylation (MetO) of proteins by excessive reactive oxygen species (ROS) can impair the basic functionality of essential cellular proteins, contributing to heart failure. Methionine sulfoxide reductase B2 (MsrB2) can reverse oxidation induced MetO in mitochondrial proteins, so we investigated its role in diabetic cardiomyopathy. We observed that DM-induced heart damage in diabetic mice model is characterized by increased ROS, increased protein MetO with mitochondria structural pathology, and cardiac fibrosis. In addition, MsrB2 was significantly increased in mouse DM cardiomyocytes, supporting the induction of a protective process. Further, MsrB2 directly induces Parkin and LC3 activation (mitophagy markers) in cardiomyocytes. In MsrB2, knockout mice displayed abnormal electrophysiological function, as determined by ECG analysis. Histological analysis confirmed increased cardiac fibrosis and disrupted cardiac tissue in MsrB2 knockout DM mice. We then corroborated our findings in human DM heart samples. Our study demonstrates that increased MsrB2 expression in the heart protects against diabetic cardiomyopathy.Graphic

ADRB2 and ADCY9 Sequence Variations in Brazilian Asthmatic Patients.

Asthma is a chronic inflammatory respiratory condition, characterized by variable airflow limitation, leading to clinical symptoms such as dyspnea and chest tightness. These symptoms result from an underlying inflammatory process. The β2 agonists are bronchodilators prescribed for the relief of the disease. Nevertheless, their efficacy exhibits substantial interindividual variability. Currently, there is widespread recognition of the association between specific genetic variants, predominantly located within the ADRB2 and ADCY9 genes and their efficacy. This association, usually represented by the presence of non-synonymous single nucleotide polymorphisms (SNPs) have a strong impact in the protein functionality. The prevalence of these mutations varies based on the ethnic composition of the population and thus understanding the profiles of variability in different populations would contribute significantly to standardizing the use of these medications. In this study, we conducted a sequence-based genotyping of the relevant SNPs within the ADRB2 and ADCY9 genes in patients undergoing treatment with bronchodilators and/or corticosteroids at two healthcare facilities in the state of Rio de Janeiro, Brazil. We investigated the presence of c.46A>G, c.79C>G, c.252G>A, and c.491C>T SNPs within the ADRB2, and c.1320018 A>G within the ADCY9. Our results were in line with existing literature data with both for individuals in Brazil and Latin American.

Biallelic variants in COX18 cause a mitochondrial disorder primarily manifesting as peripheral neuropathy.

Defects in mitochondrial dynamics are a common cause of Charcot-Marie-Tooth disease (CMT), while primary deficiencies in the mitochondrial respiratory chain (MRC) are rare and atypical for this etiology. This study aims to report COX18 as a novel CMT-causing gene. This gene encodes an assembly factor of mitochondrial Complex IV (CIV) that translocates the C-terminal tail of MTCO2 across the mitochondrial inner membrane. Exome sequencing was performed in four affected individuals. The patients and available family members underwent thorough neurological and electrophysiological assessment. The impact of one of the identified variants on splicing, protein levels, and mitochondrial bioenergetics was investigated in patient-derived lymphoblasts. The functionality of the mutant protein was assessed using a Proteinase K protection assay and immunoblotting. Neuronal relevance of COX18 was assessed in a Drosophila melanogaster knockdown model. Exome sequencing coupled with homozygosity mapping revealed a homozygous splice variant c.435-6A>G in COX18 in two siblings with early-onset progressive axonal sensory-motor peripheral neuropathy. By querying external databases, we identified two additional families with rare deleterious biallelic variants in COX18 . All affected individuals presented with axonal CMT and some patients also exhibited central nervous system symptoms, such as dystonia and spasticity. Functional characterization of the c.435-6A>G variant demonstrated that it leads to the expression of an alternative transcript that lacks exon 2, resulting in a stable but defective COX18 isoform. The mutant protein impairs CIV assembly and activity, leading to a reduction in mitochondrial membrane potential. Downregulation of the COX18 homolog in Drosophila melanogaster displayed signs of neurodegeneration, including locomotor deficit and progressive axonal degeneration of sensory neurons. Our study presents genetic and functional evidence that supports COX18 as a newly identified gene candidate for autosomal recessive axonal CMT with or without central nervous system involvement. These findings emphasize the significance of peripheral neuropathy within the spectrum of primary mitochondrial disorders and the role of mitochondrial CIV in the development of CMT. Our research has important implications for the diagnostic workup of CMT patients.

Influence of salts on the protein composition and functionality of gluten

Different salts were added to gluten to investigate the effects of different cations on a fully developed gluten network. The chloride salts KCl, NaCl, MgCl2, CaCl2 were mixed with pre-isolated wet gluten in a low and high dose, and the gluten was dried at 40 °C and 80 °C to yield vital gluten. The impact of the individual cations on the gluten protein composition and functionality was determined by analysis of chemical and rheological properties of vital and wet gluten. All cations influenced the gluten protein composition and the rheological behaviour. While the observed changes could not be attributed to the order of the Hofmeister series, monovalent, kosmotropic cations K+ and Na+ and divalent, chaotropic cations Mg2+ and Ca2+ showed similar behaviour in terms of protein composition and functional properties. Salts therefore have an influence on the gluten protein composition of a fully developed gluten network and gluten protein composition and functionality can be altered by an after-treatment process in a targeted way.

Impact of non‐thermal plasma generated using air and nitrogen on functional properties of milk protein dispersions

AbstractThis study focuses on improving the functionalities of milk protein concentrate (MPC) using a nonthermal plasma jet and plasma‐activated water (PAW) with atmospheric air and nitrogen as source gases. The 5% and 10% MPC dispersions were directly treated with a plasma jet, and PAW was used to make the MPC dispersions. The dispersions were analyzed for changes in protein structure and functional properties. The treatment altered the secondary structure of MPC protein structure by increasing β‐components and changing the order of random coils. The solubility of the PAW‐treated 5% protein dispersions doubled due to plasma‐induced modification of hydrophilic and covalent bonds of the protein, but this increase was not significant for the 10% dispersions due to less hydration. Emulsifying capacity increases by around 7% for plasma jet and PAW with air, owing to hydrophobicity on the particle surface. The gelation capacity and heat coagulation time rise by almost twice; however, foaming capacity decreases, indicating protein structural modifications and aggregations caused by plasma exposure. The viscosity of the 5% dispersions decreased due to high solubility, while that of the 10% dispersions increased due to less hydration. Principle component analysis was used to correlate the change in functionality with different operating parameters. In conclusion, this study illustrates that the functional properties of MPC can be significantly modified through plasma treatment. The observed changes depend on several factors, including the mode of plasma exposure, the source gas used to generate the plasma, and the concentration of the protein solution.Practical applicationsMilk protein concentrate (MPC) is a promising ingredient in food products such as cheese, cultured dairy items, nutritional goods, infant milk formulas, ice cream, dairy‐based drinks, sports beverages, and a variety of health‐focused products. However, the application is profoundly hindered due to its poor solubility and solubility‐related functional properties. MPC powders lose functionalities during manufacturing and gradually lose them again during processing and storage. This study explores the potential of non‐thermal plasma to improve the functional properties of proteins. This study explores the potential of two different discharges: plasma jet and plasma‐activated water (PAW), using atmospheric air and nitrogen as source gases. The findings of this study would also help to understand the types of plasma discharge (jet vs PAW) and types of sources of gases that can be used in industrial applications. Some optimization parameters of this study can be used for scaling up the plasma processing of milk or dairy products. In addition, PAW is being very well studied to improve food safety, and this study would provide information on the physicochemical properties of MPC. Therefore, it would also help to understand how to apply non‐thermal plasma to achieve both microbial and physical effects.

Meat quality and safety issues during high temperatures and cutting-edge technologies to mitigate the scenario.

Climate change, driven by the natural process of global warming, is a worldwide issue of significant concern because of its adverse effects on livestock output. The increasing trend of environmental temperature surging has drastically affected meat production and meat product quality, hence result in economic losses for the worldwide livestock business. Due to the increasing greenhouse gas emissions, the situation would get prolonged, and heat exposure-related stress is expected to worsen. Heat exposure causes metabolic and physiological disruptions in livestock. Ruminants and monogastric animals are very sensitive to heat stress due to their rate of metabolism, development, and higher production levels. Before slaughter, intense hot weather triggers muscle glycogen breakdown, producing pale, mushy, and exudative meat with less water-holding capacity. Animals exposed to prolonged high temperatures experience a decrease in their muscle glycogen reserves, producing dry, dark, and complex meat with elevated final pH and increased water-holding capacity. Furthermore, heat stress also causes oxidative stresses, especially secondary metabolites from lipid oxidation, severely affects the functionality of proteins, oxidation of proteins, decreasing shelf life, and food safety by promoting exfoliation and bacterial growth. Addressing the heat-related issues to retain the sustainability of the meat sector is an essential task that deserves an inclusive and comprehensive approach. Considering the intensity of the heat stress effects, this review has been designed primarily to examine the consequences of hot environment temperatures and related stresses on the quality and safety of meat and secondarily focus on cutting edge technology to reduce or alleviate the situational impact.

Modulation of physico-chemical and technofunctional properties of quinoa protein isolate: Effect of precipitation acid

The typically low solubility and gelation capacity of plant proteins can impose challenges in the design of high-quality plant-based foods. The acid used during the precipitation step of plant protein isolate extraction can influence protein functionality. Here, acetic acid and citric acid were used to extract quinoa protein isolate (QPI) from quinoa flour, as these acids are more kosmotropic than the commonly used HCl, promoting the stabilisation of the native protein structure. While proximate analysis showed that total protein was similar for the three isolates, precipitation with kosmotropic acids increased soluble protein, which correlated positively with gel strength. Microstructure analysis revealed that these gels contained a less porous protein network with lipid droplet inclusions. This study shows that the choice of precipitation acid offers an opportunity to tailor the properties of quinoa protein isolate for application, a strategy that is likely applicable to other plant protein isolates.

Characterization of biotinylated human ACE2 and SARS-CoV-2 Omicron BA.4/5 spike protein reference materials

Accurate diagnostic and serology assays are required for the continued management of the COVID-19 pandemic yet spike protein mutations and intellectual property concerns with antigens and antibodies used in various test kits render comparability assessments difficult. As the use of common, well-characterized reagents can help address this lack of standardization, the National Research Council Canada has produced two protein reference materials (RMs) for use in SARS-CoV-2 serology assays: biotinylated human angiotensin-converting enzyme 2 RM, ACE2-1, and SARS-CoV-2 Omicron BA.4/5 spike protein RM, OMIC-1. Reference values were assigned through a combination of amino acid analysis via isotope dilution liquid chromatography tandem mass spectrometry following acid hydrolysis, and ultraviolet–visible (UV–Vis) spectrophotometry at 280 nm. Vial-to-vial homogeneity was established using UV–Vis measurements, and protein oligomeric status, monitored by size exclusion liquid chromatography (LC-SEC), was used to evaluate transportation, storage, and freeze–thaw stabilities. The molar protein concentration in ACE2-1 was 25.3 ± 1.7 µmol L−1 (k = 2, 95% CI) and consisted almost exclusively (98%) of monomeric ACE2, while OMIC-1 contained 5.4 ± 0.5 µmol L−1 (k = 2) spike protein in a mostly (82%) trimeric form. Glycoprotein molar mass determination by LC-SEC with multi-angle light scattering detection facilitated calculation of corresponding mass concentrations. To confirm protein functionality, the binding of OMIC-1 to immobilized ACE2-1 was investigated with surface plasmon resonance and the resulting dissociation constant, KD ~ 4.4 nM, was consistent with literature values.Graphical

Novel Z-DNA binding domains in giant viruses

Z-nucleic acid structures play vital roles in cellular processes and have implications in innate immunity due to their recognition by Zα domains containing proteins (Z-DNA/Z-RNA binding proteins, ZBPs). Although Zα domains have been identified in six proteins, including viral E3L, ORF112, and I73R, as well as, cellular ADAR1, ZBP1, and PKZ, their prevalence across living organisms remains largely unexplored. In this study, we introduce a computational approach to predict Zα domains, leading to the revelation of previously unidentified Zα domain-containing proteins in eukaryotic organisms, including non-metazoan species. Our findings encompass the discovery of new ZBPs in previously unexplored giant viruses, members of the Nucleocytoviricota phylum. Through experimental validation, we confirm the Zα functionality of select proteins, establishing their capability to induce the B-to-Z conversion. Additionally, we identify Zα-like domains within bacterial proteins. While these domains share certain features with Zα domains, they lack the ability to bind to Z-nucleic acids or facilitate the B-to-Z DNA conversion. Our findings significantly expand the ZBP family across a wide spectrum of organisms and raise intriguing questions about the evolutionary origins of Zα-containing proteins. Moreover, our study offers fresh perspectives on the functional significance of Zα domains in virus sensing and innate immunity and opens avenues for exploring hitherto undiscovered functions of ZBPs.

Unveiling differential impact of heat and microwave extraction treatments on the structure, functionality, and digestibility of jack bean proteins extracted under varying extraction pH

The poor extractability and digestibility of jack beans restrict their application in food systems. Thermal treatment could be a processing tool to disrupt the compact conformation of the plant matrix and inactivate inherent antinutrients. Therefore, this research investigated the impact of conventional heat-aided (HA-) and microwave-aided (MA-) extraction treatments on the structure, functional properties, and digestibility of jack bean protein concentrate (JBPC) under varying extraction pH. The novelty brought by the present study is establishing the thermal treatment/extraction pH combinations for improving techno-functionalities and digestibility of JBPC. Heat (50 °C for 1 h) and sequential microwave power (400 W, 600 W, and 800 W for 5 min) at three extraction pH (9.0, 10.0, and 11.0) were studied. Upon increasing extraction pH, a significant decrease in the protein content, and β-Sheet structure was observed, in the order of pH 11.0 > 10.0 > 9.0. JBPC extracted using HA treatments displayed the highest contents of surface hydrophobicity (90.02) and sulfhydryl groups. In functional properties, MA-extracted JBPC under 400 W showed significantly improved solubility (93.45 %), emulsifying activity index (45.23 m2/g), and foaming capacity (141.70 %) when compared to other thermal treatments. The degree of hydrolysis result revealed that MA treatment improved the JBPC in vitro digestibility at a low power level of 400 W. These findings suggest that MA extraction treatment can improve the functional and nutritional properties of JBPC regardless of the extraction pH, and thus, expand the potential application in food systems.

Protein-Chlorogenic Acid Interactions: Mechanisms, Characteristics, and Potential Food Applications.

The interactions between proteins and chlorogenic acid (CGA) have gained significant attention in recent years, not only as a promising approach to modify the structural and techno-functional properties of proteins but also to enhance their bioactive potential in food systems. These interactions can be divided into covalent (chemical or irreversible) and non-covalent (physical or reversible) linkages. Mechanistically, CGA forms covalent bonds with nucleophilic amino acid residues of proteins by alkaline, free radical, and enzymatic approaches, leading to changes in protein structure and functionality, such as solubility, emulsification properties, and antioxidant activity. In addition, the protein-CGA complexes can be obtained by hydrogen bonds, hydrophobic and electrostatic interactions, and van der Waals forces, each offering unique advantages and outcomes. This review highlights the mechanism of these interactions and their importance in modifying the structural, functional, nutritional, and physiological attributes of animal- and plant-based proteins. Moreover, the potential applications of these protein-CGA conjugates/complexes are explored in various food systems, such as beverages, films and coatings, emulsion-based delivery systems, and so on. Overall, this literature review provides an in-depth overview of protein-CGA interactions, offering valuable insights for future research to develop novel protein-based food and non-food products with improved nutritional and functional characteristics.

Particle size reduction influences starch and protein functionality, and nutritional quality of stone milled whole wheat flour from hard red spring wheat

Flour particle size (PS) distribution plays a crucial role in determining the functional properties of starch, protein, and influences the nutritional properties, which ultimately is reflected in the end-product quality. For stone-milled whole wheat flour (WWF) bakers often prefer finer PS for improved color and texture, despite this can sometimes negatively affect other quality aspects. Therefore, understanding the contribution of PS reduction on the functional properties of stone-milled WWF is crucial. This study investigated Hard Red Spring (HRS) WWF of which the mean PS was reduced from 151 μm to 117 μm, the possible finest PS by a “Kombi mill type A 500 MSM” stone mill. PS reduction increased starch damage from 6.58% to 6.71%. Also, the amylose content reduced from 31.7% to 29.4%. However, an increase in syneresis, solubility, oil-holding capacity, and peak viscosity was observed. Glutopeak and wet gluten showed an increased gluten strength. Glutenin/gliadin, polymeric/monomeric protein ratios, and percentage of unextractable polymeric protein were increased by 2.10%, 4.11%, and 4.55%, respectively, indicating increased availability of proteins with relatively larger molecular sizes by PS reduction. The relative proportion of glutenin and gliadin subgroups were also changed. Dietary fiber and resistant starch contents were found to be lower. However, the reduction in phytic acid and FODMAPs is considered beneficial. PS reduction ultimately improved bread loaf volume and crumb structure. Overall, PS reduction of WWF by stone-milling brought positive changes to several functional properties of protein and starch and positively improved the dough rheology and end-product quality.

Chromophore-Assisted Light Inactivation for Protein Degradation and Its Application in Biomedicine.

The functional investigation of proteins holds immense significance in unraveling physiological and pathological mechanisms of organisms as well as advancing the development of novel pharmaceuticals in biomedicine. However, the study of cellular protein function using conventional genetic manipulation methods may yield unpredictable outcomes and erroneous conclusions. Therefore, precise modulation of protein activity within cells holds immense significance in the realm of biomedical research. Chromophore-assisted light inactivation (CALI) is a technique that labels photosensitizers onto target proteins and induces the production of reactive oxygen species through light control to achieve precise inactivation of target proteins. Based on the type and characteristics of photosensitizers, different excitation light sources and labeling methods are selected. For instance, KillerRed forms a fusion protein with the target protein through genetic engineering for labeling and inactivates the target protein via light activation. CALI is presently predominantly employed in diverse biomedical domains encompassing investigations into protein functionality and interaction, intercellular signal transduction research, as well as cancer exploration and therapy. With the continuous advancement of CALI technology, it is anticipated to emerge as a formidable instrument in the realm of life sciences, yielding more captivating outcomes for fundamental life sciences and precise disease diagnosis and treatment.

ProBASS - a language model with sequence and structural features for predicting the effect of mutations on binding affinity.

Protein-protein interactions (PPIs) govern virtually all cellular processes. Even a single mutation within PPI can significantly influence overall protein functionality and potentially lead to various types of diseases. To date, numerous approaches have emerged for predicting the change in free energy of binding (ΔΔGbind) resulting from mutations, yet the majority of these methods lack precision. In recent years, protein language models (PLMs) have been developed and shown powerful predictive capabilities by leveraging both sequence and structural data from protein-protein complexes. Yet, PLMs have not been optimized specifically for predicting ΔΔGbind. We developed an approach to predict effects of mutations on PPI binding affinity based on two most advanced protein language models ESM2 and ESM-IF1 that incorporate PPI sequence and structural features, respectively. We used the two models to generate embeddings for each PPI mutant and subsequently fine-tuned our model by training on a large dataset of experimental ΔΔGbind values. Our model, ProBASS (Protein Binding Affinity from Structure and Sequence) achieved a correlation with experimental ΔΔGbind values of 0.83 ± 0.05 for single mutations and 0.69 ± 0.04 for double mutations when model training and testing was done on the same PDB. Moreover, ProBASS exhibited very high correlation (0.81 ± 0.02) between prediction and experiment when training and testing was performed on a dataset containing 2325 single mutations in 132 PPIs. ProBASS surpasses the state-of-the-art methods in correlation with experimental data and could be further trained as more experimental data becomes available. Our results demonstrate that the integration of extensive datasets containing ΔΔGbind values across multiple PPIs to refine the pre-trained PLMs represents a successful approach for achieving a precise and broadly applicable model for ΔΔGbind prediction, greatly facilitating future protein engineering and design studies.

Enhancing functionality and bioactivity of walnut protein through limited enzyme digestion.

Walnut protein (WP) is recognized as a valuable plant protein. However, the poor solubility and functional properties limit its application in the food industry. It is a great requirement to improve the physicochemical properties of WP. Following a 90 min restricted enzymatic hydrolysis period, the solubility of WP significantly increased from 3.24% to 54.54%, with the majority of WP hydrolysates (WPHs) possessing a molecular weight exceeding 50 kDa. Circular dichroism spectra showed that post-hydrolysis, the structure of the protein became more flexible, while the hydrolysis time did not significantly alter the protein's secondary structure. After hydrolysis, WP's surface hydrophobicity significantly increased from 2279 to 6100. Furthermore, WPHs exhibited a strong capacity for icariin loading and micelle formation with critical micelle concentration values of 0.71, 0.99 and 1.09 mg mL-1, respectively. Moreover, similar immuno-enhancement activities were observed in WPHs. After exposure to WPHs, the pinocytosis of RAW264.7 macrophages was significantly improved. WPH treatment also increased the production of nitric oxide, interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α) in macrophages. Up-regulation of mRNA expressions of IL-6, inducible nitric oxide synthase (iNOS) and TNF-α was observed in a dose-dependent manner. The enhancement of functionality and bioactivity in WP can be achieved through the application of limited enzyme digestion with trypsin. This process effectively augments the nutritional value and utility of the protein, making it a valuable component in various dietary applications. © 2024 Society of Chemical Industry.