Protein Functionality Research Articles

Affinity Purification of a 6X-His-Tagged Protein using a Fast Protein Liquid Chromatography System.

Functional characterization of proteins requires them to be expressed and purified in substantial amounts with high purity to perform biochemical assays. The Fast Protein Liquid Chromatography (FPLC) system allows high-resolution separation of complex protein mixtures. By adjusting various parameters in FPLC, such as selecting the appropriate purification matrix, regulating the protein sample's temperature, and managing the sample's flow rate onto the matrix and the elution rate, it is possible to ensure the protein's stability and functionality. In this protocol, we will demonstrate the versatility of the FPLC system to purify 6X-His-tagged flap endonuclease 1 (FEN1) protein, produced in bacterial cultures. To improve protein purification efficiency, we will focus on multiple considerations, including proper column packing and preparation, sample injection using a sample loop, flow rate of sample application to the column, and sample elution parameters. Finally, the chromatogram will be analyzed to identify fractions containing high yields of protein and considerations for proper recombinant protein long-term storage. Optimizing protein purification methods is crucial for improving the precision and reliability of protein analysis.

Pea protein isolate-soluble soybean polysaccharides electrostatic assembly: effect of pH, biopolymer mass ratio and heat treatment.

In past years, thousands of protein-polysaccharide complexes have been investigated to modify protein characteristics and functionality in food systems. However, the interaction between pea protein isolate (PPI) and soluble soybean polysaccharide (SSPS) has not been thoroughly characterized yet. In the present study, the phase behavior of PPI and SSPS mixtures was analyzed as a function of PPI:SSPS mixing ratio (1:1 to 1:0.10) and pH (7.0 to 2.0), showing that these biopolymers could be electrostatically assembled at 1:1 to 1:0.25 mixing ratios and 4.0 to 3.0 pH values. Then, the characteristics of the PPI-SSPS complexes were studied before and after heating (90 °C and 30 min) by ζ-potential, surface hydrophobicity, protein solubility, particle size distribution and physical stability for 56 days. By lowering the pH and PPI:SSPS mixing ratio, the complexes showed increased solubility, changed 𝜁-potential and higher physical stability. By heating, the complexes presented increased hydrophobicity and physical stability. Overall, PPI-SSPS complexes increased the protein solubility, reduced the particle size, and changed both the ζ-potential and the surface hydrophobicity with respect to PPI control, allowing stabilization of the colloidal system and broadening the possible applications of these high-quality proteins in acidic food systems. © 2024 Society of Chemical Industry.

The C-terminal Region of D-DT Regulates Molecular Recognition for Protein-Ligand Complexes.

Systematic analysis of molecular recognition is critical for understanding the biological function of macromolecules. For the immunomodulatory protein D-dopachrome tautomerase (D-DT), the mechanism of protein-ligand interactions is poorly understood. Here, 17 carefully designed protein variants and wild type (WT) D-DT were interrogated with an array of complementary techniques to elucidate the structural basis of ligand recognition. Utilization of a substrate and two selective inhibitors with distinct binding profiles offered previously unseen mechanistic insights into D-DT-ligand interactions. Our results demonstrate that the C-terminal region serves a key role in molecular recognition via regulation of the active site opening, protein-ligand interactions, and conformational flexibility of the pocket's environment. While our study is the first comprehensive analysis of molecular recognition for D-DT, the findings reported herein promote the understanding of protein functionality and enable the design of new structure-based drug discovery projects.

Exploring the Nutritional Potential and Functionality of Hemp and Rapeseed Proteins: A Review on Unveiling Anti-Nutritional Factors, Bioactive Compounds, and Functional Attributes.

Plant-based proteins, like those derived from hemp and rapeseed can contribute significantly to a balanced diet and meet human daily nutritional requirements by providing essential nutrients such as protein, fiber, vitamins, minerals, and antioxidants. According to numerous recent research papers, the consumption of plant-based proteins has been associated with numerous health benefits, including a reduced risk of chronic diseases such as heart disease, diabetes, and certain cancers. Plant-based diets are often lower in saturated fat and cholesterol and higher in fiber and phytonutrients, which can support overall health and well-being. Present research investigates the nutritional attributes, functional properties, and potential food applications of hemp and rapeseed protein for a potential use in new food-product development, with a certain focus on identifying anti-nutritional factors and bioactive compounds. Through comprehensive analysis, anti-nutritional factors and bioactive compounds were elucidated, shedding light on their impact on protein quality and digestibility. The study also delves into the functional properties of hemp and rapeseed protein, unveiling their versatility in various food applications. Insights from this research contribute to a deeper understanding of the nutritional value and functional potential of hemp and rapeseed protein, paving the way for their further utilization in innovative food products with enhanced nutritional value and notable health benefits.

Protein Functionality is Critical for the Texturization Process during High Moisture Extrusion Cooking

Protein Functionality is Critical for the Texturization Process during High Moisture Extrusion Cooking

Computational Analysis of Deleterious nsSNPs in INS Gene Associated with Permanent Neonatal Diabetes Mellitus.

Insulin gene mutations affect the structure of insulin and are considered a leading cause of neonatal diabetes and permanent neonatal diabetes mellitus PNDM. These mutations can affect the production and secretion of insulin, resulting in inadequate insulin levels and subsequent hyperglycemia. Early discovery or prediction of PNDM can aid in better management and treatment. The current study identified potential deleterious non-synonymous single nucleotide polymorphisms nsSNPs in the INS gene. The analysis of the nsSNPs in the INS gene was conducted using bioinformatics tools by implementing computational algorithms including SIFT, PolyPhen2, SNAP2, SNPs & GO, PhD-SNP, MutPred2, I-Mutant, MuPro, and HOPE tools to investigate the prediction of the potential association between nsSNPs in the INS gene and PNDM. Three mutations, C96Y, P52R, and C96R, were shown to potentially reduce the stability and function of the INS protein. These mutants were subjected to MDSs for structural analysis. Results suggested that these three potential pathogenic mutations may affect the stability and functionality of the insulin protein encoded by the INS gene. Therefore, these changes may influence the development of PNDM. Further researches are required to fully understand the various effects of mutations in the INS gene on insulin synthesis and function. These data can aid in genetic testing for PNDM to evaluate its risk and create treatment and prevention strategies in personalized medicine.

Characterization of structural and functional properties of soybean 11S globulin during renaturation after denaturation induced by changes in pH.

This study explored the denaturation of 11S globulin, a protein known for its diverse functional properties in soy protein applications, at pH 3.0 and pH 10.0, followed by a gradual return to pH 7.0 to facilitate renaturation. It investigated the structural and functional changes during renaturation induced by a change in pH, revealing the stabilization mechanism of 11S globulin. The findings revealed that during pH adjustment to neutral, the denatured soybean 11S globulin - resulting from alkaline (pH 10.0) or acidic (pH 3.0) treatments - experienced a refolding of its extended tertiary structure to varying extents. The particle size and the proportions of α-helix and β-sheet in the secondary structure aligned progressively with those of the natural-state protein. However, for the alkali-denatured 11S, the β-sheet content decreased upon adjustment to neutral, whereas an increase was observed for the acid-denatured 11S. In terms of functional properties, after alkaline denaturation, the foaming capacity (FC) and emulsifying activity index (EAI) of 11S increased by 1.4 and 1.2 times, respectively, in comparison with its native state. The solubility, foamability, and emulsifiability of the alkali-denatured 11S gradually diminished during renaturation but remained superior to those of the native state. Conversely, these properties showed an initial decline, followed by an increase during renaturation triggered by pH neutralization. This research contributes to the enhancement of protein functionality, offering a theoretical foundation for the development of functional soy protein products and expanding their potential applications. © 2024 Society of Chemical Industry.

Molecular dynamics simulation of the effect of temperature on the conformation of ubiquitin protein.

Ubiquitin, a ubiquitous small protein found in all living organisms, is crucial for tagging proteins earmarked for degradation and holds pivotal importance in biomedicine. Protein functionality is intricately linked to its structure. To comprehend the impact of diverse temperatures on ubiquitin protein structure, our study delved into the energy landscape, hydrogen bonding, and overall structural stability of ubiquitin protein at varying temperatures. Through meticulous analysis of root mean square deviation and root mean square fluctuation, we validated the robustness of the simulation conditions employed. Within our simulated system, the bonding energy and electrostatic potential energy exhibited linear augmentation, while the van der Waals energy demonstrated a linear decline. Additionally, our findings highlighted that the α-Helix secondary structure of the ubiquitin protein gradually transitions toward helix destabilization under high-temperature conditions. The secondary structure of ubiquitin protein experiences distinct changes under varying temperatures. The outcomes of our molecular simulations offer a theoretical framework that enhances our comprehension of how temperature impacts the structural stability of ubiquitin protein. These insights contribute not only to a deeper understanding of iniquity's behavior but also hold broader implications in the realm of biomedicine and beyond. All the MD simulations were performed using the GROMACS software with GROMOS96 force field and SPC for water. The ubiquitin protein was put in the center of a cubic box with a length of 8nm, a setting that allowed > 0.8nm in the minimal distance between the protein surface and the box wall. To remove the possible coordinate collision of the configurations, in the beginning, the steepest descent method was used until the maximum force between atoms was under 100kJ/mol·nm with a 0.01nm step size. Minimization was followed by 30ps of position-restrained MD simulation. The protein was restrained to its initial position, and the solvent was freely equilibrated. The product phase was obtained with the whole system simulated for 10ns without any restraint using an integral time step of 1fs with different temperatures. The cutoff for short-range electronic interaction was set to 1.5nm. The long-range interactions were treated with a particle-mesh Ewald (PME) method with a grid width of 1.2nm.

A new preparation method of covalent annular nanodiscs based on MTGase

The preservation of the native conformation and functionality of membrane proteins has posed considerable challenges. While detergents and liposome reconstitution have been traditional approaches, nanodiscs (NDs) offer a promising solution by embedding membrane proteins in phospholipids encircled by an amphipathic helical protein MSP belt. Nevertheless, a drawback of commonly used NDs is their limited homogeneity and stability. In this study, we present a novel approach to construct covalent annular nanodiscs (cNDs) by leveraging microbial transglutaminase (MTGase) to catalyze isopeptide bond formation between the side chains of terminal amino acids, specifically Lysine (K) and Glutamine (Q). This methodology significantly enhances the homogeneity and stability of NDs. Characterization of cNDs and the assembly of membrane proteins within them validate the successful reconstitution of membrane proteins with improved homogeneity and stability. Our findings suggest that cNDs represent a more suitable tool for investigating interactions between membrane proteins and lipids, as well as for analyzing membrane protein structures.

Cold‐pressing, ethanol defatting, and saline extraction enhances properties of protein products from new pennycress varieties (covercress™)

AbstractPennycress (Thlaspi arvense L.), a winter oilseed and cover crop, is a source of novel proteins and oil for biofuel. New yellow‐seeded pennycress specialty varieties, named covercress™, were developed via conventional breeding and gene editing, but protein characteristics are still unknown. This work evaluated two covercress lines, TT8 and Y1126, for protein extraction and functionality, and the combination of cold‐pressing, alcohol‐defatting, and saline extraction to produce a protein that could align better with clean labeling. Seeds were first cold‐pressed in a tubular radial expeller then defatted at 60°C with anhydrous ethanol (‐Eth) or hexane (‐Hex) until ≤0.8% residual oil. Protein was extracted from defatted press cake (PC) using the saline method (0.1 M NaCl, 1: 10 w/v, 50°C, 2 h) for hexane‐defatted wild‐type pennycress (WTP) seed meal and PC. TT8 PC had 33%–67% more globulin and glutelin than WTP PC, but ethanol defatting reduced albumin + globulin amounts by 14%–32%. TT8 PC protein recoveries (63% and 40%) were 2‐ to 3‐fold greater than that of Y1126 PC‐Eth and their extracts had greater purity (85%–91% vs. 70% protein). Y1126 PC‐Eth protein showed a nearly constant 68%–70% solubility from pH 2 to 10, but TT8 PC‐Eth protein was more soluble in acidic pH (87%–90% solubility). Y1126 PC‐Eth protein showed greater foaming capacity (146–150 mL), while TT8 PC‐Eth protein had superior emulsifying properties (EAI 141–236 m2/g protein and ESI 13–26 min). This work demonstrated the enhanced functionality of TT8 and Y1126 proteins produced from an environmentally friendly and industrially relevant method.

A novel pathogenic SLC12A5 missense variant in epilepsy of infancy with migrating focal seizures causes impaired KCC2 chloride extrusion.

The potassium-chloride co-transporter 2, KCC2, is a neuron-specific ion transporter that plays a multifunctional role in neuronal development. In mature neurons, KCC2 maintains a low enough intracellular chloride concentration essential for inhibitory neurotransmission. During recent years, pathogenic variants in the KCC2 encoding gene SLC12A5 affecting the functionality or expression of the transporter protein have been described in several patients with epilepsy of infancy with migrating focal seizures (EIMFS), a devastating early-onset developmental and epileptic encephalopathy. In this study, we identified a novel recessively inherited SLC12A5 c.692G>A, p. (R231H) variant in a patient diagnosed with severe and drug-resistant EIMFS and profound intellectual disability. The functionality of the variant was assessed in vitro by means of gramicidin-perforated patch-clamp experiments and ammonium flux assay, both of which indicated a significant reduction in chloride extrusion. Based on surface immunolabeling, the variant showed a reduction in membrane expression. These findings implicate pathogenicity of the SLC12A5 variant that leads to impaired inhibitory neurotransmission, increasing probability for hyperexcitability and epileptogenesis.

Tailored Branched Polymer-Protein Bioconjugates for Tunable Sieving Performance.

Protein-polymer conjugates combine the unique properties of both proteins and synthetic polymers, making them important materials for biomedical applications. In this work, we synthesized and characterized protein-branched polymer bioconjugates that were precisely designed to retain protein functionality while preventing unwanted interactions. Using chymotrypsin as a model protein, we employed a controlled radical branching polymerization (CRBP) technique utilizing a water-soluble inibramer, sodium 2-bromoacrylate. The green-light-induced atom transfer radical polymerization (ATRP) enabled the grafting of branched polymers directly from the protein surface in the open air. The resulting bioconjugates exhibited a predetermined molecular weight, well-defined architecture, and high branching density. Conformational analysis by SEC-MALS validated the controlled grafting of branched polymers. Furthermore, enzymatic assays revealed that densely grafted polymers prevented protein inhibitor penetration, and the resulting conjugates retained up to 90% of their enzymatic activity. This study demonstrates a promising strategy for designing protein-polymer bioconjugates with tunable sieving behavior, opening avenues for applications in drug delivery and biotechnology.

Enhancing the functionality of pea proteins by conjugation with propylene glycol alginate via transacylation reaction assisted with ultrasonication

Pea proteins lack the desirable functional characteristics for food and beverage applications. In this study, transacylation reaction assisted with ultrasonication was used to glycate pea proteins with propylene glycol alginate to enhance their functional properties. The reaction was carried out at pH 11.0 for different pea protein isolate: propylene glycol alginate mass ratios and time durations in a sonic bath at 40 °C. Glycation was confirmed in gel electrophoresis, and ultrasonication enhanced the glycation, with optimal degrees of glycation observed at 45 min reaction time and mass ratios of 2:1 (37.73%) and 1:1 (35.96%). The transacylation reaction increased random coil content of pea proteins by 28% and enhanced their solubility by 2.02 times at pH 7.0, water holding capacity by >50% at pH 7.0, foaming properties, emulsifying properties, and heat stability. This study offers a novel approach that can enhance functionality and applicability of pea proteins.

Integrative analysis unveils ECM signatures and pathways driving hepatocellular carcinoma progression: A multi-omics approach and prognostic model development.

Liver hepatocellular carcinoma (LIHC) is a highly lethal form of cancer that is among the deadliest cancer types globally. In terms of cancer-related mortality rates, liver cancer ranks among the top three, underscoring the severity of this disease. Insufficient analysis has been conducted to fully understand the potential value of the extracellular matrix (ECM) in immune infiltration and the prognostic stratification of LIHC, despite its recognised importance in the development of this disease. The scRNA-seq data of GSE149614 was used to conduct single-cell analysis on 10 LIHC samples. CellChat scores were calculated for seven cell populations in the descending cohort to investigate cellular communication, while PROGENy scores were calculated to determine tumour-associated pathway scores in different cell populations. The pathway analysis using GO and KEGG revealed the enrichment of ECM-associated genes in the pathway, highlighting the potential role of the ECM in LIHC development. By utilizing the TCGA-LIHC cohort, an ECM-based prognostic model for LIHC was developed using Lasso regression. Immune infiltration scores were calculated using two methods, and the performance of the ECM-related risk score was evaluated using an independent cohort from the CheckMate study. To determine the precise expression of ECM-associated risk genes in LIHC, we evaluated hepatocellular carcinoma cell lines using a range of assays, including Western blotting, invasion assays and Transwell assays. Using single-cell transcriptome analysis, we annotated the spatially-specific distribution of major immune cell types in single-cell samples of LIHC. The main cell types identified and annotated included hepatocytes, T cells, myeloid cells, epithelial cells, fibroblasts, endothelial cells and B cells. The utilisation of cellchat and PROGENy analyses enabled the investigation and unveiling of signalling interactions, protein functionalities and the prominent influential pathways facilitated by the primary immune cell types within the LIHC. Numerous tumour pathways, including PI2K, EGFR and TGFb, demonstrated a close correlation with the involvement of ECM in LIHC. Moreover, an evaluation was conducted to assess the primary ECM-related functional changes and biological pathway enrichment in LIHC. Differential genes associated with ECM were identified and utilised to create prognostic models. The prognostic stratification value of these models for LIHC patients was confirmed through validation in multiple databases. Furthermore, through immune infiltration analysis, it was discovered that ECM might be linked to the irregular expression and regulation of numerous immune cells. Additionally, histone acetylation was mapped against gene mutation frequencies and differential expression profiles. The prognostic stratification efficacy of the ECM prediction model constructed in the context of PD-1 inhibitor therapy was also examined, and it exhibited strong stratification performance. Cellular experiments, including Western blotting, invasion and Transwell assays, revealed that ECM-associated risk genes have a promoting effect on the development of LIHC. The creation of biomarkers for LIHC using ECM-related genes unveiled substantial correlations with immune microenvironmental infiltration and functional mutations in various tumour pathways. This enlightens us to the possibility that the influence of ECM on tumours may extend beyond simply promoting the fibrotic process and the stromal composition of tumours.

Elucidating the Impact of Deleterious Mutations on IGHG1 and Their Association with Huntington's Disease.

Huntington's disease (HD) is a chronic, inherited neurodegenerative condition marked by chorea, dementia, and changes in personality. The primary cause of HD is a mutation characterized by the expansion of a triplet repeat (CAG) within the huntingtin gene located on chromosome 4. Despite substantial progress in elucidating the molecular and cellular mechanisms of HD, an effective treatment for this disorder is not available so far. In recent years, researchers have been interested in studying cerebrospinal fluid (CSF) as a source of biomarkers that could aid in the diagnosis and therapeutic development of this disorder. Immunoglobulin heavy constant gamma 1 (IGHG1) is one of the CSF proteins found to increase significantly in HD. Considering this, it is reasonable to study the potential involvement of deleterious mutations in IGHG1 in the pathogenesis of this disorder. In this study, we explored the potential impact of deleterious mutations on IGHG1 and their subsequent association with HD. We evaluated 126 single-point amino acid substitutions for their impact on the structure and functionality of the IGHG1 protein while exploiting multiple computational resources such as SIFT, PolyPhen-2, FATHMM, SNPs&Go mCSM, DynaMut2, MAESTROweb, PremPS, MutPred2, and PhD-SNP. The sequence- and structure-based tools highlighted 10 amino acid substitutions that were deleterious and destabilizing. Subsequently, out of these 10 mutations, eight variants (Y32C, Y32D, P34S, V39E, C83R, C83Y, V85M, and H87Q) were identified as pathogenic by disease phenotype predictors. Finally, two pathogenic variants (Y32C and P34S) were found to reduce the solubility of the protein, suggesting their propensity to form protein aggregates. These variants also exhibited higher residual frustration within the protein structure. Considering these findings, the study hypothesized that the identified variants of IGHG1 may compromise its function and potentially contribute to HD pathogenesis.

Effect of pH‐shifting treatment on the structural characteristics and nutritional quality of the ultrasonically extracted protein isolate from soybean meal

AbstractSoybean meal is an underutilized byproduct of the soybean oil processing industry, which is rich in high quality protein but mostly used as an animal feed. Valorization of soybean meal on a large scale is possible by extracting protein isolate and modifying its structural characteristics through pH‐shifting or ultrasonic treatment, which has a direct association with the better functional properties of protein isolate. The present study aimed to evaluate the impact of pH‐shifting treatment on the structural characteristics and nutritional quality of ultrasonically extracted soybean meal protein isolate (SMPI). The results showed that the pH shifted SMPI had higher hydrophobicity (60.5–104.3) and free sulfhydryl group (22.67–24.45 μmol/g) than without pH shifted SMPI (53.5 and 19.67 μmol/g, respectively). The fluorescence intensity of the SMPI treated at extreme acidic and alkaline pH was higher than that of other pH‐treated samples. The ꞵ‐sheet (39.68%) components of SMPI treated at pH 10 showed the highest value when compared to other pH‐treated (38.18–39.26%). The alkaline pH‐treated sample had higher concentration of essential amino acids (36.16 g/100 g) than other acidic or near neutral pH‐treated sample (30.06–32.30 g/100 g). The quality parameters such as biological value (67.62), and amino acid index (72.77) were higher for the SMPI treated at pH 10 as compared to the SMPI treated at other pH conditions. Hence, the pH‐treatment method can be utilized as an effective technique to improve the characteristics of SMPI, which will increases its applications in various food sectors.Practical ApplicationsThe current investigation demonstrated that pH‐shifting treatment had a substantial impact on the structural and nutritional quality of the soybean meal protein isolate extracted by ultrasonication. Improvements in soybean meal protein's surface hydrophobicity, free sulfhydryl groups, and secondary structural components will expand its uses in the dairy, bread, meat, and infant food development industries, among other food sectors as these structural changes improve the functionality of protein. Furthermore, the treatment of soybean meal protein isolate with pH shifting led to a considerable increase in nutritional quality, as measured by the essential amino acid composition, essential amino acid index, and protein efficiency ratio, which is expected to increase its utilization in novel food product development.

Computational screening of damaging nsSNPs in human SOD1 genes associated with amyotrophic lateral sclerosis identifies destabilising effects of G38R and G42D mutations through in silico evaluation.

Amyotrophic lateral sclerosis (ALS), a complicated neurodegenerative disorder affected by hereditary and environmental variables, is a condition. In this study, the genetic makeup of ALS is investigated, with a focus on the SOD1 gene's single-nucleotide polymorphisms (SNPs) and their ability to affect disease risk. Eleven high-risk missense variations that may impair the functionality of the SOD1 protein were discovered after a thorough examination of SNPs in the SOD1 gene. These mutations were chosen using a variety of prediction approaches, highlighting their importance in the aetiology of ALS. Notably, it was discovered that the stability of the SOD1 wild-type protein structure was compromised by the G38R and G42D SOD1 variants. Additionally, Edaravone, a possible ALS medication, showed a greater affinity for binding mutant SOD1 structures, pointing to potential personalised treatment possibilities. The high-risk SNPs discovered in this investigation seem to have functional effects, especially on the stability of proteins and their interactions with other molecules. This study clarifies the complex genetics of ALS and offers insights into how these genetic variations may affect the effectiveness of therapeutic interventions, particularly in the context of edaravone. In this study advances our knowledge of the genetic mechanisms causing ALS vulnerability and prospective therapeutic strategies. Future studies are necessary to confirm these results and close the gap between individualised clinical applications and improved ALS care.

Insights into enzymatic hydrolysis: Exploring effects on antioxidant and functional properties of bioactive peptides from Chlorella proteins

Chlorella protein hydrolysate (CPH) is highly valued for its protein content, solubility, and functionality. Our main aim is to produce CPH via enzymatic hydrolysis using pepsin, alkaline, trypsin, and pancreatic enzymes and to analyze its amino acid composition, antioxidant activity, functional, and physiological properties. After the extraction and preparation of bioactive peptides (BAPs) derived from Chlorella protein, they were enzymatically hydrolyzed using the mentioned enzymes, and the degree of hydrolysis (DH) was evaluated. Our results showed that samples fabricated with trypsin and alkaline enzymes had the highest water-holding capacity (WHC) (3.8 g water/g dry matter) and oil-holding capacity (OHC) (5.7 g oil/g dry matter), respectively. Enzymatic hydrolysis with alkaline enzyme and trypsin showed the strongest radical scavenging activities of DPPH (83.2%) and ABTS (77.5%), respectively. Additionally, hydroxyl radical scavenging activity (HRSA) and reducing power of crude protein increased after enzymatic hydrolysis. Enzymatic hydrolysis also increased the metal-chelating activity. Based on these findings, it can be concluded that CPH has the best potential in improving the nutritional and functional properties of food ingredients and products.

Computational Characterization of Membrane Proteins as Anticancer Targets: Current Challenges and Opportunities.

Cancer remains a leading cause of mortality worldwide and calls for novel therapeutic targets. Membrane proteins are key players in various cancer types but present unique challenges compared to soluble proteins. The advent of computational drug discovery tools offers a promising approach to address these challenges, allowing for the prioritization of "wet-lab" experiments. In this review, we explore the applications of computational approaches in membrane protein oncological characterization, particularly focusing on three prominent membrane protein families: receptor tyrosine kinases (RTKs), G protein-coupled receptors (GPCRs), and solute carrier proteins (SLCs). We chose these families due to their varying levels of understanding and research data availability, which leads to distinct challenges and opportunities for computational analysis. We discuss the utilization of multi-omics data, machine learning, and structure-based methods to investigate aberrant protein functionalities associated with cancer progression within each family. Moreover, we highlight the importance of considering the broader cellular context and, in particular, cross-talk between proteins. Despite existing challenges, computational tools hold promise in dissecting membrane protein dysregulation in cancer. With advancing computational capabilities and data resources, these tools are poised to play a pivotal role in identifying and prioritizing membrane proteins as personalized anticancer targets.

Identification and functional analysis of DNA methylation-related enzyme gene family in Eleutherococcus senticosus

Eleutherococcus senticosus, a medicinal and edible plant recognized historically in East Asia, is characterized by a rich composition of saponins and other biologically active ingredients. In this study, 11 cytosine-5 DNA methyltransferases (C5-MTase) and 6 demethylases (dMTase) genes were identified within the genome of E. senticosus. Specifically, two major EsC5-MTases (EsMET1a and EsCMT3b) and two EsdMTases (EsROS1a and EsDME1) were screened through correlation analysis, examining the relationship between their gene expression levels and DNA methylation ratio within E. senticosus genome. Promoter function analysis revealed that the expression of these four prominent genes was regulated by abiotic stresses such as drought and light. In vitro catalytic validation demonstrated the functionality of EsMET1a, EsCMT3b, EsROS1a, and EsDME1 proteins in modifying DNA methylation patterns of key enzyme genes associated with saponin synthesis in E. senticosus. Additionally, transient in vivo overexpression of the four central genes could alter the saponin content by modulating the DNA methylation levels and secondary metabolic processes in E. senticosus. Molecular docking studies further elucidated the possible mechanism of DNA methylation and demethylation catalyzed by these four primary proteins.