Protein Secondary Structure Research Articles

Monomer unfolding of a bacterial ESCRT-III superfamily member is coupled to oligomer disassembly.

The inner membrane associated protein of 30 kDa (IM30), a member of the endosomal sorting complex required for transport (ESCRT-III) superfamily, is crucially involved in the biogenesis and maintenance of thylakoid membranes in cyanobacteria and chloroplasts. In solution, IM30 assembles into various large oligomeric barrel- or tube-like structures, whereas upon membrane binding it forms large, flat carpet structures. Dynamic localization of the protein in solution, to membranes and changes of the oligomeric states are crucial for its in vivo function. ESCRT-III proteins are known to form oligomeric structures that are dynamically assembled from monomeric/smaller oligomeric proteins, and thus these smaller building blocks must be assembled sequentially in a highly orchestrated manner, a still poorly understood process. The impact of IM30 oligomerization on function remains difficult to study due to its high intrinsic tendency to homo-oligomerize. Here, we used molecular dynamics simulations to investigate the stability of individual helices in IM30 and identified unstable regions that may provide structural flexibility. Urea-mediated disassembly of the IM30 barrel structures was spectroscopically monitored, as well as changes in the protein's tertiary and secondary structure. The experimental data were finally compared to a three-state model that describes oligomer disassembly and monomer unfolding. In this study, we identified a highly stable conserved structural core of ESCRT-III proteins and discuss the advantages of having flexible intermediate structures and their putative relevance for ESCRT-III proteins.

From Zebrafish To Humans: In Silico Comparative Study of RAD50 Sequences

DNA damage, particularly the occurrence of DNA double-strand breaks (DSBs), presents a significant hazard to the integrity and viability of cells. Improper repair of DSBs can result in chromosomal alterations, oncogenic changes, or cell demise. The MRE11-RAD50-NBS1 (MRN) complex plays a crucial role in DNA repair and signaling under the Ataxia Telangiectasia Mutated (ATM) kinase regulation. In this study, we employed comprehensive computational techniques to analyze the structure of RAD50 in Danio rerio (Zebrafish), utilized as a model organism. Additionally, we conducted in silico assessments of RAD50 from both Zebrafish and humans, comparing their characteristics. The substantial sequence resemblance between DrRAD50 and HsRAD50 suggests that DrRAD50 could potentially serve as a valuable model for HsRAD50. However, it is important to acknowledge that sequence similarity alone does not necessarily imply functional equivalence. Further functional studies are needed to confirm the extent of their functional similarities. By examining the secondary and tertiary protein structures of RAD50, we observed a notable likeness between Zebrafish and Human RAD50 proteins. In silico analysis demonstrated that the sequence of RAD50 in zebrafish shares 70% similarity with the human RAD50 protein.

A comprehensive and single-use foot-and-mouth disease sero-surveillance prototype employing rationally designed multiple viral antigens

Foot-and-mouth disease (FMD) is a great havoc in agri-business-based countries like Bangladesh, for which existing detection system limits the identification and differentiation of serotypes. In this study, an engineered platform was introduced incorporating serotype-specific FMDV VP1 (structural), serotype-independent VP2 (structural) and 3AB (non-structural) proteins for holistic detection. VP1 sequences were engineered combining sequences of BAN/TA/Dh-301/2016 (serotype O), BAN/CH/Sa-304/2016 (serotype A) and BAN/DH/Sa-318/2016 (serotype Asia1). Consensus 3AB sequence was constructed from the selected prevalent viral genomes. Both VP1 and 3AB along with designed VP2 sequences were optimized for codon usage bias, stable mRNA, secondary and tertiary protein structure. Proteins were synthesized in pET-21a ( +) plasmid vector followed by transformation of Escherichia coli BL21(DE3) and IPTG-induced- expression. The western blot analysis of engineered proteins showed that purified VP1 prominently bound to anti-VP1 antibodies in vaccinated sera, whereas 3AB and VP2 bound anti-3AB and anti-VP2 antibodies, respectively from infected cattle sera, all previously collected during epidemiological investigation. Furthermore, dot blot hybridization confirmed efficient antibody capture ability of the membrane-immobilized proteins. This holistic diagnostic platform justifies a comprehensive prototype diagnostic kit that would be cost-effective and efficient for serotype specific and non-specific FMDV sero-surveillance.

Novel insights into fouling mechanisms in anaerobic acidification membrane bioreactor: The leading role of pH value

Anaerobic acidification membrane bioreactors (AAMBRs) have recently emerged as effective systems for recovering volatile fatty acids (VFAs) from municipal wastewater. However, membrane fouling remains a critical challenge, with its underlying mechanisms not yet fully understood. Given its importance in inhibiting methanogenic bacteria and stabilizing VFAs production, this study explores the direct and indirect effects of pH on membrane fouling mechanisms in AAMBRs. The results demonstrated that compared to pH 7, the fouling potential of anaerobic sludge was significantly higher at pH levels of 5 and 10 owing to a decrease of sludge floc size and an increase of soluble microbial products (SMP) especially proteins. Analytical techniques such as confocal laser scanning microscopy (CLSM), fourier transform infrared spectroscopy (FTIR), and fluorescence excitation-emission matrix (F-EEM) analyses revealed a substantial increase in organic foulants particularly proteins on the membrane surface at pH levels of 5 and 10. Circular dichroism (CD) spectroscopy further indicated a significant change in protein secondary structure, specifically an increase in α-helix content under extreme pH conditions. Furthermore, the extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) theory indicated that elevated protein concentrations enhance the adhesion of sludge and SMP to membrane surfaces. Insights from the Flory-Huggins theory demonstrated that variations in protein structure significantly contribute to increased filtration resistance within the gel layer. Both experimental data and theoretical models underscore the dual role of pH in optimizing VFAs production and managing membrane fouling, offering insights for enhancing AAMBR performance and mitigating fouling issues.

ILMCNet: A Deep Neural Network Model That Uses PLM to Process Features and Employs CRF to Predict Protein Secondary Structure.

Protein secondary structure prediction (PSSP) is a critical task in computational biology, pivotal for understanding protein function and advancing medical diagnostics. Recently, approaches that integrate multiple amino acid sequence features have gained significant attention in PSSP research. We aim to automatically extract additional features represented by evolutionary information from a large number of sequences while simultaneously incorporating positional information for more comprehensive sequence features. Additionally, we consider the interdependence between secondary structures during the prediction stage. To this end, we propose a deep neural network model, ILMCNet, which utilizes a language model and Conditional Random Field (CRF). Protein language models (PLMs) pre-trained on sequences from multiple large databases can provide sequence features that incorporate evolutionary information. ILMCNet uses positional encoding to ensure that the input features include positional information. To better utilize these features, we propose a hybrid network architecture that employs a Transformer Encoder to enhance features and integrates a feature extraction module combining a Convolutional Neural Network (CNN) with a Bidirectional Long Short-Term Memory Network (BiLSTM). This design enables deep extraction of localized features while capturing global bidirectional information. In the prediction stage, ILMCNet employs CRF to capture the interdependencies between secondary structures. Experimental results on benchmark datasets such as CB513, TS115, NEW364, CASP11, and CASP12 demonstrate that the prediction performance of our method surpasses that of comparable approaches. This study proposes a new approach to PSSP research and is expected to play an important role in other protein-related research fields, such as protein tertiary structure prediction.

Ischemic stroke susceptibility associated with ALPK1 single nucleotide polymorphisms by inhibiting URAT1 in uric acid hemostasis

ObjectivesIschemic stroke (IS) prevalence rising annually, the necessity of discovering non-interventional genetic influences is progressing. Single nucleotide polymorphism (SNP) plays a pivotal role in stable inheritance of disease susceptibility. Based on the relationship between Alpha- Kinase 1 (ALPK1) and traditional IS risk factors especially hyperuricemia, our study investigated the association and function of ALPK1 SNPs with IS susceptibility. MethodsA case-control study of 1539 patients and 933 controls from northeast China was conducted. Genotyping information of ALPK1 rs2074379 and rs2074388 was collected. Four types of plasmids including rs2074379/rs2074388 G/G, A/G, G/A, and A/A were transfected into 293T cells to observe ALPK1 and SLC22A12 expression. Possible ALPK1 structures of different SNPs were predicted online. ResultsGenotype GG (OR = 1.371, CI = 1.029–1.828, P = 0.031) and GA (OR = 1.326, CI = 1.110–1.584, P = 0.002) of rs2074379 and GA of rs2074388 (OR = 1.359, CI = 1.137–1.624, P = 0.001) were found significantly susceptible to IS, with G allele on sites to be a risk allele. Rs2074379 had a multiplicative interaction with hyperuricemia (OR = 1.637, CI = 1.157–2.315, P = 0.005). Uric acid levels differed in genotypes (P < 0.001). The expression of ALPK1 (P < 0.01) and SLC22A12 in membrane urate transporter 1 (URAT1) protein (P < 0.05) functionally changed with G allele on either site. With glycine changing into aspartic acid at rs2074388, the protein secondary structure changed, but the ALPK1 protein subtype remained still. ConclusionsALPK1 rs2074379 and rs2074388 SNPs were functionally associated with IS susceptibility. The wild allele progressed IS risk probably by reducing ALPK1 expression and inhibiting URAT1 raising the uric acid level, contributing to further exploration of pathogenetic mechanisms of stroke.Chinese Clinical Trial Registration number: ChiCTR-COC-17013559.

Functional characteristics and molecular structural modification of plant proteins. Review

Protein preparations from plant raw materials are widely used in the food industry as improvers, replacers or enrichers for products. However, their functional properties, as a rule, are less pronounced than those of proteins of animal origin. The aim of the review is to analyze and summarize the results of investigations dedicated to studying and characterizing the main functional properties of plant proteins (hydration, solubility, water binding capacity, fat binding capacity and gel-forming capacity, stability of emulsions, foams, rheological properties, texturization) and their modification. The objects of the research were scientific publications, most of which were published in 2017–2024. Functional properties of proteins were characterized; their dependence on the nature and variety of crop, methods of extraction, technological factors of processing and methods of modification was revealed. The search and selection of papers were carried out in the bibliographic databases eLIBRARY.RU, RSCI, Google Scholar, Scopus, Web of Science, Elsevier, and PubMed. Data analysis was performed with their systematization, generalization, intermediate conclusions and general conclusion. The special attention was paid to chemical, physical, physico-chemical and enzymatic methods for modification of protein properties, their advantages and disadvantages, as well as the interrelation of structural and physico-chemical features of proteins with their functional properties. The main regularities were revealed for an effect of modification methods on the secondary and tertiary structures of proteins, surface hydrophobicity, the ratio from fractions, aggregation, denaturation and biological activity obtained by the modern methods of investigations (IR‑spectroscopy, fluorescent microscopy, SDS-PAGE, circular dichroism, spectrophotometry and so on). It has been concluded that it is necessary to carry out further investigations aimed to studying interrelation of molecular structural features of proteins with indicators of functionality and regularities of their behavior in food systems due to an increase in the production of protein preparations from alternative raw materials (pea, chickpea, sunflower, kidney bean, rice and others). Based on the revealed and newly obtained theoretical information, the targeted modification and regulation of properties of protein ingredients for production of high-quality foods are possible.

Cloning and Expression Analysis of ATG8 (Autophagy-Related 8) Gene Family in Solanaceae.

The autophagy-related gene family ATG8 (Autophagy-related 8) plays an important role in plant growth, development, and stress response. In this study, 15 ATG8 gene family sequences were amplified from Solanaceae, namely tobacco, tomato, and pepper, using RT-PCR to evaluate their basic properties, protein structure, and function, as well as the role of ATG8 in autophagy. The physicochemical properties, the predicted secondary and tertiary protein structures, subcellular localisation, gene structures, conserved motifs, and phylogenetic relationships of the ATG8 genes were analysed using bioinformatic techniques, and their expression patterns under sericin-induced plant disease resistance were investigated by RT-qPCR. The lengths of these proteins ranged from 79 to 120 aa, while their predicted molecular weights and isoelectric points (PI) ranged from 9283.62 to 13,778.74 and 6.32 to 11.44, respectively. The majority of the proteins were localised in the nucleus or chloroplasts. Conserved protein motifs and various cis-regulatory elements in the protein, with a wide range of related functions, were identified. The ATG8 gene family members showed expression changes after treatment with osthole, which induces disease resistance in tobacco, tomato, and pepper. These findings provide a foundation for further analyses of the ATG8 gene family in Solanaceae and the mechanism underlying the response to adverse conditions.

Magnetic field improves the quality of frozen tilapia fillets by decreasing the ice crystals during freezing process

SummaryIn this study, the alternating magnetic field (AMF) with frequency of 50, 100, 150, 200 and 250 Hz at magnetic field intensity of 5 mT was used to assist the freezing of tilapia fillets, with no magnetic field (NMF) as a control group. The evaluation of thawed tilapia fillets encompassed an assessment of freezing curve, texture, microstructure, moisture state and protein structure, followed by a subsequent analysis of their correlation. The findings showed that the application of a magnetic field during the freezing process yielded favourable outcomes in enhancing the overall quality of tilapia fillets. Among them, 200 Hz had the best effect. Under the condition, the frozen tilapia fillets assisted by magnetic field showed the shortest freezing time, the least decrease in hardness and elasticity and the best chewiness after thawing. The size of the ice crystals generated during freezing was small and uniform, and the fractal dimension of the frozen sections was the highest. Muscle tissue was the least damaged, which led to the improvement of its water‐holding capacity. Magnetic field‐assisted freezing was found to maintain the α‐helix and β‐sheet in the secondary structure of proteins. The correlation analysis showed that cohesion, elasticity, fractal dimension, FD, A2, A22 and β‐turn were closely related to the quality changes of tilapia fillets after magnetic field treatment.

Translation of Mutant Repetitive Genomic Sequences in Hirsutella sinensis and Changes in the Secondary Structures and Functional Specifications of the Encoded Proteins.

Multiple repetitive sequences of authentic genes commonly exist in fungal genomes. AT-biased genotypes of Ophiocordyceps sinensis have been hypothesized as repetitive pseudogenes in the genome of Hirsutella sinensis (GC-biased Genotype #1 of O. sinensis) and are generated through repeat-induced point mutation (RIP), which is charactered by cytosine-to-thymine and guanine-to-adenine transitions, concurrent epigenetic methylation, and dysfunctionality. This multilocus study examined repetitive sequences in the H. sinensis genome and transcriptome using a bioinformatic approach and revealed that 8.2% of the authentic genes had repetitive copies, including various allelic insertions/deletions, transversions, and transitions. The transcripts for the repetitive sequences, regardless of the decreases, increases, or bidirectional changes in the AT content, were identified in the H. sinensis transcriptome, resulting in changes in the secondary protein structure and functional specification. Multiple repetitive internal transcribed spacer (ITS) copies containing multiple insertion/deletion and transversion alleles in the genome of H. sinensis were GC-biased and were theoretically not generated through RIP mutagenesis. The repetitive ITS copies were genetically and phylogenetically distinct from the AT-biased O. sinensis genotypes that possess multiple transition alleles. The sequences of Genotypes #2-17 of O. sinensis, both GC- and AT-biased, were absent from the H. sinensis genome, belong to the interindividual fungi, and differentially occur in different compartments of the natural Cordyceps sinensis insect-fungi complex, which contains >90 fungal species from >37 genera. Metatranscriptomic analyses of natural C. sinensis revealed the transcriptional silencing of 5.8S genes in all C. sinensis-colonizing fungi in natural settings, including H. sinensis and other genotypes of O. sinensis. Thus, AT-biased genotypes of O. sinensis might have evolved through advanced evolutionary mechanisms, not through RIP mutagenesis, in parallel with GC-biased Genotype #1 of H. sinensis from a common genetic ancestor over the long course of evolution.

Interactions of the Biphenylene Network with α-Helical and β-Sheet Proteins: Molecular Dynamics Simulations.

In recent years, nanomaterials have been widely used in the biomedical field. The biphenylene network is a highly promising planar carbon nanomaterial. To better explore its biomedical applications, we need to understand the biological effects of the biphenylene network. To investigate the biological effects of the novel nanomaterial biphenylene network, we used molecular dynamics simulations to study the interactions of the novel planar carbon nanomaterial biphenylene network with α-helical and β-sheet proteins. We found that both types of proteins adsorb flatly on the surface of the biphenylene network; the strong van der Waals interaction is the main adsorption force, while π-π stacking also provides an auxiliary force for the adsorption. When the HP35 protein whose secondary structure is an α-helix was adsorbed on biphenylene network, the entire structure of α-helix 2 was disrupted and α-helix 3 partly recovered its helical structure after being disrupted. In contrast to the β-sheet YAP65 protein, only part of the structure of β-sheet 1 was disrupted. Therefore, the biocompatibility of the biphenylene network with the β-sheet YAP65 protein is better than that of the α-helical HP35 protein, which may be due to the different surface curvature of the protein's secondary structure. Our research promotes the application of the biphenylene network in biomedicine and provides a theoretical basis and experimental direction for practical experiments.

The effects of ultrasound-assisted glycation on the allergenicity and functional properties of peanut proteins

This study investigated the effects of ultrasound-assisted glycation on the allergenicity and functional properties of peanut proteins. Results showed that ultrasound-assisted glycation increased the degree of glycation reaction of peanut proteins significantly (P < 0.05). ELISA results indicated that the binding of peanut allergens with serum immunoglobulin G (IgG) and immunoglobulin E (IgE) was significantly decreased (P < 0.05). Furthermore, secondary structure analysis revealed a significant increase in β-sheet content, alongside decreases in α-helix, β-turn, and random coil contents (P < 0.05). In addition, intrinsic fluorescence intensity, surface hydrophobicity, and ultraviolet (UV) spectra intensity were diminished (P < 0.05), indicating notable changes in both secondary and tertiary structures of peanut proteins. Moreover, emulsification property, antioxidant activity and in vitro digestibility of peanut proteins showed the most obvious improvements following ultrasound-assisted glycation, and the solubility was increased while turbidity was decreased significantly (P < 0.05). In conclusion, this study demonstrated that ultrasound-assisted glycation not only effectively reduced the allergenicity of peanut allergens, but also improved the overall functional properties of peanut proteins, and the changes in sensitization and functional properties might be closely related to structural changes. This study will provide a theoretical basis for the development of peanut products.

Raman Microspectroscopy of Hair: Low-Frequency Markers of Protein Secondary Structure.

Low-frequency intervals that can be used to study the secondary structure of proteins are determined. Compared are Ramanspectra of keratins from unpigmented human hair, measured in two experimental configurations: with excitation radiation coaxial with the hair and perpendicular to it. Based on the polarization sensitivity, the bands peaked at 150 and 221 cm-1 are assigned to vibrations of α-helical structures. The comparison of Raman spectra of hair fragments with different contents of secondary structure elements shows that the vibrations of β-structure are manifested in a spectral interval of 270-340 cm-1. The results obtained for a particular object (hair keratin) can be used in the study of the secondary structure of proteins.

In silico and in vitro evaluation of a PE38 and Nb-based recombinant immunotoxin targeting the GRP78 receptor in cancer cells.

Cancer is a global health problem despite the most developed therapeutic modalities. The delivery of specific therapeutic agents to a target increases the effectiveness of cancer treatment by reducing side effects and post-treatment issues. Our aim in this study was to design a recombinant protein consisting of nanobody molecules and exotoxin that targets the surface GRP78 receptor on tumor cells. Bioinformatics methods make drug design and recombinant protein evaluation much easier before the laboratory steps. Two constructs were designed from a single-variable domain on heavy chain nanobody domains and PE toxin domains II, Ib, and III. The physicochemical properties, secondary structure, and solubility of the chimeric protein were analyzed using different software. Prostate cancer DU-145 and breast cancer MDA-MB-468 cell lines were used as GRP78-positive and negative controls, respectively. Accordingly, the cytotoxicity, binding affinity, cell internalization, and apoptosis were evaluated using MTT, enzyme-linked immunosorbent assay, and western blot. The results showed that in the DU-145 cell line, the cytotoxicity of two recombinant immunotoxins is dose and time-dependent. In MDA-MB-468 and HEK-293 cells, such an event does not occur. It is possible that two constructs designed for immunotoxins can attach to GRP78-positive cancer cells and then eradicate cancer cells by internalization and apoptosis. As our in vitro results were in line with in silico data confirming the Bioinformatics predictions, it can be concluded that the designed recombinant immunotoxins may exhibit therapeutic potential against GRP78-positive tumor cells.

Frabrication of carboxymethylchitin nanofibers and fish gelatin hybrid gels with robust gel performance

Compared to animal gelatin, the application of fish gelatin (FG) in the food industry is limited due to its lower gel hardness, gelation temperature, and melting temperature. To address these issues, we developed hybrid gels using carboxymethyl chitin nanofibers (CMC-NFs) with FG to enhance its gel properties. The chitin was carboxymethylated by monochloroacetic acid, increasing the negative potential from −6 mV to −35 mV. This modified chitin was then defibrillated into CMC-NFs through high-pressure homogenization to improve its water dispersibility. The addition of 0.1% CMC-NFs significantly increased the hardness of FG gels from 533 g to 989 g, which was notably higher than the ∼600 g hardness of porcine gelatin. Additionally, the gelation and melting temperatures of FG reached 17 °C and 32 °C, respectively, which are very close to the 20 °C and 35 °C of porcine gelatin. Mechanistic studies revealed that FG and CMC-NFs (0.1%) molecules formed a synergistic gel network, facilitated by hydrogen bonding and hydrophobic interactions. This interaction significantly increased the α-helix content in the secondary structure of the FG protein from 15.26% to 21.18%, thereby enhancing the FG-dominated three-dimensional network structure with CMC-NF molecules. Increasing the concentration of CMC-NFs further elevated the gel's melting temperature while reducing its hardness due to phase separation. This study not only presents a viable method for enhancing the gelling properties of modified FG but also offers a feasible solution for expanding FG's applications in the food industry.

Cryoprotective effect of magnetic field-assisted freezing in combination with curdlan on myofibrillar protein of Litopenaeus vannamei: Oxidative aggregation, protein structure and thermal stability

To counteract the negative effects of conventional freezing methods on frozen surimi products, the present study investigated the effects of magnetic field (MF) freezing in combination with different amounts of curdlan (CUR) on oxidative denaturation, structural alterations, and thermal stability of myofibrillar protein (MP) in shrimp surimi. The results indicated that the intervention of magnetic fields alone improved the quality of frozen muscle proteins. Under the dual intervention of magnetic field-assisted freezing and CUR, small ice crystals formed with MF6 treatment resulted in significantly lower solubility, turbidity, and mean particle size than the control group (p < 0.05). Moreover, the oxidation of MP was also significantly slowed down by inhibiting the formation of hydrophobic groups and carbonyl groups, maintaining a high content of sulfhydryl groups. MF6 also exhibited a high Ca2+-ATPase activity. The α-helix content, the increase in fluorescence intensity under this condition also tend to make the secondary and tertiary structures of myofibrillar protein more stable. Meanwhile, electrophoretic profiles and CLSM showed that this condition maintains the integrity of the MP. In addition, the MF6 samples also had high protein thermal stability. However, excess CUR reduces the excellence of MP cryoprotection. As a result, MF6 has better protection and improvement effects on protein function, structure and thermal stability, and CUR was also found to have the potential for cryoprotectant development.

Interactions with peanut protein isolate regulate the bioaccessibility of cyanidin-3-O-glucoside: Multispectral analysis, simulated digestion, and molecular dynamic simulation

Anthocyanins are susceptible to degradation owing to environmental factors. Combining them with proteins can improve their stability; however, the interaction mechanism is difficult to elucidate. This study used multispectral and molecular dynamics simulations and molecular docking methods to investigate the interaction mechanism between peanut protein isolate (PPI) and cyanidin-3-O-glucoside (C3G). The UV absorption peak and PPI turbidity increased, while the fluorescence intensity decreased with greater C3G content. Protein secondary structure changes suggested that PPI and C3G coexisted in spontaneous covalent and non-covalent interactions via static quenching. The complex structures were stable over time and C3G stably bound to the peanut globulin Ara h 3 cavity through hydrogen bonding and hydrophobic interactions. Furthermore, PPI enhanced the C3G antioxidant activity and bioaccessibility by increasing its retention rate during in-vitro simulated digestion. This study elucidates the binding mechanism of PPI and C3G and provides insight into applications of the complex in food development.

Protein digestibility in wheat noodles: The inhibitory effect and its mechanism of wheat bran dietary fiber

This study investigated the effects of different wheat flour extraction rate (35–95%) on the protein digestibility of those noodles. And to further elucidate the internal mechanism of above phenomenon, wheat flour with different amounts of wheat bran dietary fiber (WBDF) was produced by adding endogenous WBDF. Results indicated that protein digestibility rose significantly with increasing flour extraction rate, peaking at 91.85% at 80% extraction, before trending downward to 85.71% at 95% extraction. Further, among noodles containing different WBDF content, increasing WBDF content to 6% enhanced the formation of β-sheets, boosting I755 levels and reducing I854/I830 levels, thus decreasing protein digestibility. As WBDF content rose further, it promoted transition from β-sheets to β-turn, decreasing I755 and increasing I854/I830, enhancing protein digestibility slightly. The changes indicated that low level of WBDF induced a more compact protein secondary structure to inhibit protein digestion. Conversely, in noodles with high level of WBDF (>6%), the looser protein secondary structure partially alleviated the inhibitory effect of WBDF on protein digestion, which was caused by part of WBDF penetrating the protein's hydrophobic core. Moreover, the static quenching effect of WBDF on pepsin hydrolysis sites through hydrophobic interaction, especially the tyrosine, was another significant factor inhibiting protein digestion.

Quantification of soluble protein content and characterization of protein secondary structure by Raman spectroscopy combined with chemometrics

In the large-scale industrialized production of soymilk, the accurate monitoring of protein content and its secondary structure is crucial to guarantee product quality and enhance nutritional value, while traditional protein detection methods have significant limitations. In this study, Raman spectroscopy was used to characterize the changes in the relative content of protein secondary structures during boiling, in which the α-helix structure was converted to other unstable secondary structures, indicating that the protein was thermally denatured. The study also accurately predicted the soluble protein content of soymilk for the first time by combining Raman spectroscopy and chemometrics based on algorithms such as Partial Least Squares (PLS), Least Squares Support Vector Machines (LSSVM), and Artificial Neural Networks (ANN). The results showed that the relative percentage deviation (RPD) values of all models were greater than 2, indicating that the models all possessed a certain degree of robustness; The PLS-based regression prediction model (with an average RPD value of 3.5592 and an average R2p of 0.9597) had the best overall prediction. The study's results can guide the soymilk production industry into online monitoring of soymilk quality.

COSMIC Database and Structural Modeling Analysis of CYP2D6 Mutations in Human Cancers.

Single nucleotide polymorphisms (SNPs) in cytochrome P450 (CYP450) enzymes alter the metabolism of a variety of drugs. Numerous medications, including chemotherapies, are metabolized by CYP450 enzymes, making the expression of this suite of enzymes in tumor cells relevant to prescription regimens for cancer patients. We analyzed the characteristics of mutations of the CYP2D6 enzymes in cancer patients obtained from the Catalogue of Somatic Mutations in Cancer (COSMIC), including mutation type, age of the patient, tissue type, and histology. Mutations were analyzed through the Cancer-Related Analysis of Variants Toolkit (CRAVAT) software along with CHASM and VEST4 algorithms to determine the likelihood of being a driver and/or pathogenic mutation. For mutations with significant CHASM and VEST4 scores, structural analysis of each corresponding mutant protein was performed. The effect of each mutation was evaluated for its impact on the overall protein stability and ligand binding using Foldit Standalone and SwissDock, respectively. Structural analysis revealed that several missense mutations in CYP2D6 resulted in altered stability after energy minimization. Three missense mutations of CYP2D6 significantly altered docking stability and those located on alpha-helices near the docking site had a more significant impact than those not found in secondary protein structures. In conclusion, we have identified a series of mutations to CYP2D6 enzymes with possible relevance to cancer pathologies. Significance Statement CYP2D6 is responsible for the metabolism of many anti-cancer drugs. This study identified and characterized a series of mutations in the CYP2D6 enzyme that occurred in tumors. We found it likely that many of these mutations would alter enzyme function, leading to changes in drug metabolism in the tumor. We provide a basis for predicting the likelihood of a patient carrying these mutations to identify patients who may benefit from a precision medicine approach to drug selection and dosing.