Protein Secondary Structure Research Articles

Enhancing Drug-Target Binding Affinity Prediction through Deep Learning and Protein Secondary Structure Integration

Background: Conventional approaches to drug discovery are often characterized by lengthy and costly processes. To expedite the discovery of new drugs, the integration of artificial intelligence (AI) in predicting drug-target binding affinity (DTA) has emerged as a crucial approach. Despite the proliferation of deep learning methods for DTA prediction, many of these methods primarily concentrate on the amino acid sequence of proteins. Yet, the interactions between drug compounds and targets occur within distinct segments within the protein structures, whereas the primary sequence primarily captures global protein features. Consequently, it falls short of fully elucidating the intricate relationship between drugs and their respective targets. Objective: This study aims to employ advanced deep-learning techniques to forecast DTA while incorporating information about the secondary structure of proteins. Methods: In our research, both the primary sequence of protein and the secondary structure of protein were leveraged for protein representation. While the primary sequence played the role of the overarching feature, the secondary structure was employed as the localized feature. Convolutional neural networks and graph neural networks were utilized to independently model the intricate features of target proteins and drug compounds. This approach enhanced our ability to capture drugtarget interactions more effectively Results: We have introduced a novel method for predicting DTA. In comparison to DeepDTA, our approach demonstrates significant enhancements, achieving a 3.9% increase in the Concordance Index (CI) and a remarkable 34% reduction in Mean Squared Error (MSE) when evaluated on the KIBA dataset. Conclusion: In conclusion, our results unequivocally demonstrate that augmenting DTA prediction with the inclusion of the protein's secondary structure as a localized feature yields significantly improved accuracy compared to relying solely on the primary structure.

Structural, techno‐functional and nutraceutical properties of lentil proteins – a concise review

SummaryLentil is one of the major pulses consumed in many parts of the world. Lentil proteins comprise primarily three fractions, viz. globulins, albumins and glutelins, each having distinct structural and functional characteristics. The secondary structure of lentil proteins is characterised by a predominance of β‐sheets, which occur in proportions up to 63% in the fractions. Protein isolates, in comparison, have up to 40% random coils, 38% sheets, 36% turns and 33% helix. Lentil proteins contain most essential amino acids, while albumins and glutelins have relatively higher content of lysine, methionine, histidine, threonine and branched‐chain amino acids. Amongst globulin proteins, vicilins have a more balanced amino acid composition than legumins. Lentil proteins also exhibit techno‐functional properties (foaming and emulsification, water and fat absorption and gelation) and may also serve as a potential source of active proteins/peptides, which make them an attractive alternative to conventional protein sources.

Effect of transglutaminase on the structure, properties and oil absorption of wheat flour

The structure, properties, as well as the oil absorption characteristics of wheat flour (WF) treated with varying concentrations of transglutaminase (TG) (0 U/g ∼ 50 U/g) were characterized. The content of free amino groups in WF modified by TG (TG-WF) decreased and protein aggregated. The isopeptide bonds and disulfide bonds played important roles in protein crosslinking. The thermal stability, the peak viscosity after gelatinization and protein secondary structure stability of TG-WF were improved. In addition, the oil absorption and surface oil content of TG-WF after frying were reduced. TG enhanced the protein-protein interactions in WF, so that protein played barrier roles in the process of high-temperature frying, protecting the starch particles covered by them from the infiltration of oil, thus reducing the oil absorption of TG-WF during frying. Among them, the oil content of TG-WF-30 U/g after frying was the lowest, which decreased by 10.73 % compared with the control group.

Molecular and biochemical characterization of a plant-like iota-class glutathione S-transferase from the halotolerant cyanobacterium Halothece sp. PCC7418.

This study identifies a unique glutathione S-transferase (GST) in extremophile using genome, phylogeny, bioinformatics, functional characterization, and RNA sequencing analysis. Five putative GSTs (H0647, H0729, H1478, H3557, and H3594) were identified in Halothece sp. PCC7418. Phylogenetic analysis suggested that H0647, H1478, H0729, H3557, and H3594 are distinct GST classes. Of these, H0729 was classified as an iota-class GST, encoding a high molecular mass GST protein with remarkable features. The protein secondary structure of H0729 revealed the presence of a glutaredoxin (Grx) Cys-Pro-Tyr-Cys (C-P-Y-C) motif that overlaps with the N-terminal domain and harbors a topology similar to the thioredoxin (Trx) fold. Interestingly, recombinant H0729 exhibited a high catalytic efficiency for both glutathione (GSH) and 1-chloro-2, 4-dinitrobenzene (CDNB), with catalytic efficiencies that were 155- and 32-fold higher, respectively compared to recombinant H3557. Lastly, the Halothece gene expression profiles suggested that antioxidant and phase II detoxification encoding genes are crucial in response to salt stress. Iota-class GST was identified in cyanobacteria. This GST exhibited a high catalytic efficiency toward xenobiotic substrates. Our findings shed light a diversified evolution of GST in cyanobacteria and provide functional dynamics of the genes encoding the enzymatic antioxidant and detoxification systems under abiotic stresses.

Textural improvement of pea protein-based high-moisture extrudates with corn zein and rice starch

High moisture extrusion allows the production of plant protein-based products, including meat analogues. Building upon our previous findings showing that zein mixed with rice starch provides the necessary textural properties to formulations, different pea protein-based formulations with varying amounts of zein and rice starch or wheat gluten (as control) were produced using high moisture extrusion and the rheological, textural, and microstructural characteristics were evaluated and associated with the secondary structure of proteins. Samples containing wheat gluten presented desirable rheological and mechanical properties in terms of texturization, which was evidenced by the generation of a layered and three-dimensional viscoelastic network. The addition of rice starch to zein significantly increased the viscoelasticity of the samples due to enhanced development of non-covalent interactions that led to higher and more stable β-sheets content and to the formation of a fibrous and layered microstructure and a 3D network nearly like those obtained with gluten. The sole replacement of pea protein by zein was not enough to develop these desired characteristics, demonstrating the importance of the non-covalent interactions between rice starch and zein for the generation of these properties. Overall, zein and rice starch improved texturization of pea protein-based gluten-free analogues made by high moisture extrusion.

Effect of stepwise cooking on the water-retention capacity and protein denaturation degree of chicken breast

This study investigated the impact of different center temperatures (60 °C, 65 °C, 70 °C) combined with low temperature long time cooking (cooking at 60 °C for 30 min or 60 min) on the water-retention capacity of chicken breasts. The effects of different heat treatment methods on microstructure, texture parameters, water content, cooking loss, color, pH value, protein denaturation degree and secondary structure content of chicken breast were analyzed. The results revealed that both center temperature and low temperature long times cooking (LTLT cooking) time significantly influenced the water-retention capacity of chicken breasts (P < 0.05). With increasing heat exposure levels, there was a corresponding rise in pH value as well as protein solubility and hydrophobicity in meat. This led to increased alignment of myofibrils along with gradual structural disruption and connective tissue efflux resulting in significant increases in meat hardness, chewiness and cooking loss (P < 0.05). However, when the center temperature reached 70 °C with an LTLT cooking time of 60 min, the muscle fiber structure is almost completely destroyed, causing the connective tissue between the muscle bundles or fibers to refill, resulting in a random coil content increase of about 2%, increased the water content by around 12% and decreased hardness by about 31%. These findings demonstrate that the group subjected to a combination treatment involving a center temperature of 70 °C and an LTLT cooking time of 60 min was effective in enhancing the water content while reducing the hardness of meat.

Geometric descriptors for beta turns.

Beta turns, in which the protein backbone abruptly changes direction over four amino acid residues, are the most common type of protein secondary structure after alpha helices and beta sheets and play key structural and functional roles. Previous work has produced classification systems for turn geometry at multiple levels of precision, but these operate in backbone dihedral-angle (Ramachandran) space, and the absence of a local Euclidean-space coordinate system and structural alignment for turns, or of any systematic Euclidean-space characterization of turn backbone shape, presents challenges for the visualization, comparison and analysis of the wide range of turn conformations and the design of turns and the structures that incorporate them. This work derives a turn-local coordinate system that implicitly aligns turns, together with a set of geometric descriptors that characterize the bulk BB shapes of turns and describe modes of structural variation not explicitly captured by existing systems. These modes are shown to be meaningful by the demonstration of clear relationships between descriptor values and the electrostatic energy of the beta-turn H-bond, the overrepresentations of key side-chain motifs, and the structural contexts of turns. Geometric turn descriptors complement Ramachandran-space classifications, and they can be used to select turn structures for compatibility with particular side-chain interactions or contexts. Potential applications include protein design and other tasks in which an enhanced Euclidean-space characterization of turns may improve understanding or performance. The web-based tools ExploreTurns, MapTurns, and ProfileTurn, available at www.betaturn.com, incorporate turn-local coordinates and turn descriptors and demonstrate their utility.

A Novel Heterozygous Intronic FBN1 Variant Contributes to Aberrant RNA Splicing in Marfan Syndrome.

Marfan syndrome (MFS) is a complex genetic systemic connective tissue disorder. It is well known that genetic factors play a critical role in the progression of MFS, with nearly all cases attributed to variants in the FBN1 gene. We investigated a Chinese family with MFS spanning two generations. Whole exome sequencing, in silico analysis, minigene constructs, transfection, RT-PCR, and protein secondary structure analysis were used to analyze the genotype of the proband and his father. The main clinical manifestations of the proband and his father were subluxation of the left lens and high myopia with pectus deformity. Whole exome sequencing identified a novel single nucleotide variant (SNV) in the FBN1 gene at a non-canonical splice site, c.443-3C>G. This variant resulted in two abnormal mRNA transcripts, leading to a frameshift and an in-frame insertion. Further invitro experiments indicated that the c.443-3C>G variant in FBN1 was pathogenic and functionally harmful. This research identified a novel intronic pathogenic FBN1: c.443-3C>G gene variant, which led to two different aberrant splicing effects. Further functional analysis expands the variant spectrum and provides a strong indication and sufficient basis for preimplantation genetic testing for monogenic disease (PGT-M).

Solution NMR backbone resonance assignment of the full-length resistance-related calcium-binding protein Sorcin.

Sorcin is a penta-EF hand calcium-binding protein that confers multidrug resistance in cancer cells. It regulates cellular Ca2+ homeostasis by interacting with calcium channels such as Ryanodine receptor 2 and Sarcoplasmic/endoplasmic reticulum Ca2+-ATPase in a calcium-dependent manner. The crystal structure of the Sorcin has been determined in both calcium-free and calcium-bound states to understand calcium-binding induced conformational change. However, due to its flexibility, most of the N-terminal domain is invisible in these crystal structures. Here we report the 1H, 13C, and 15N backbone resonance assignments of full-length Sorcin in the calcium-free state using solution NMR. The protein secondary structure was predicted based on the assigned backbone chemical shifts using TALOS+ and CSI 3.0. Our backbone resonance assignment of the full-length Sorcin provides a foundation for future NMR spectroscopic studies to uncover the mechanism of Ca2+ sensing by Sorcin.

Immobilization of Lipase from Thermomyces Lanuginosus and Its Glycerolysis Ability in Diacylglycerol Preparation.

In the glycerolysis process for diacylglycerol (DAG) preparation, free lipases suffer from poor stability and the inability to be reused. To address this, a cost-effective immobilized lipase preparation was developed by cross-linking macroporous resin with poly (ethylene glycol) diglycidyl ether (PEGDGE) followed by lipase adsorption. The selected immobilization conditions were identified as pH 7.0, 35 °C, cross-linking agent concentration 2.0%, cross-linking time 4 h, lipase amount 5 mg/g of support, and adsorption time 4 h. Enzymatic properties of the immobilized lipase were analyzed, revealing enhanced pH stability, thermal stability, storage stability, and operational stability post-immobilization. The conditions for immobilized enzyme-catalyzed glycerolysis to produce DAG were selected, demonstrating the broad applicability of the immobilized lipase. The immobilized lipase catalyzed glycerolysis reactions using various oils as substrates, with DAG content in the products ranging between 35 and 45%, demonstrating broad applicability. Additionally, the changes during the repeated use of the immobilized lipase were characterized, showing that mechanical damage, lipase leakage, and alterations in the secondary structure of the lipase protein contributed to the decline in catalytic activity over time. These findings provide valuable insights for the industrial application of lipase.

Protein Secondary Structure Prediction Using Convolutional Bidirectional GRU

In this paper, a protein secondary structure prediction method based on convolutional bidirectional GRU Model (CBi-GRU model) is adopted, which combines the advantages of sliding window in extracting local features of data. The use of CNN and Bi-GRU in the construction of the model improves the feature expression and data utilization, and improves the performance of the model. Protein data from FoxChase Institute were used, and high quality, complete and representative CullPDB dataset, CB513, CASP10 and CASP11 datasets were selected to train, test and validate the model. The results show that the proposed method achieves good prediction performance on CASP10 and CASP11 datasets, and the prediction accuracy of Q8 is 76.2% and 76.4%, respectively. Compared with RaptorX-SS, DeepCNF, CGAN-PSSP and other methods, the Q8 evaluation indicators are improved. Compared with the latest research data, our Q8 prediction accuracy is improved by 2% and 5.1%, which shows the effectiveness and superiority of the proposed model.

Hydrogen bonding patterns and cooperativity in polyproline II helical bundles

Hydrogen bond cooperativity (HBC) plays an important role in stabilizing protein assemblies built by α-helices and β-sheets, the most common secondary structures. However, whether HBC exists in other types of protein secondary structures such as polyproline II (PPII) helices remains unexplored. This is intriguing, since PPII systems as assembling blocks are continuously emerging across multiple fields. Here, using a combination of computational chemistry tools and molecular modeling corroborated by experimental observables, we characterize the distinct H-bonding patterns present in PPII helical bundles and establish that HBC stabilizes intermolecular PPII helices as seen in other protein assemblies such as amyloid fibrils. In addition to cooperative interactions in canonical CO···HN H-bonds, we show that analogous interactions in non-canonical CO···HαCα H-bonds are relevant in Gly-rich PPII bundles, thus compensating for the inability of glycine residues to create hydrophobic cores. Our results provide a mechanistic explanation for the assembly of these bundles.

Comparison of quality characteristics of reconstituted glutinous rice flour and sweet dumplings with various beans.

This study blended five types of beans-florid kidney bean, red adzuki bean, chickpea, black bean, and white kidney bean-with glutinous rice flour (GRF) to create a synergistic heat-moisture treatment (HMT). We investigated the effects of this combination on the digestibility of the glutinous rice mixture and the quality of sweet dumplings. The inclusion of beans, along with HMT, altered the granular morphology, adhesive qualities, thermal characteristics, crystallinity, and protein secondary structure of the blended powders compared to GRF. Notably, the starch granules in the glutinous rice flour with red adzuki bean (R-GRF) were more complete in morphology, compact in structure, and exhibited higher heat stabilization and crystallinity, with significant changes in protein secondary structure. These modifications resulted in a low expected glycemic index (eGI) value of 52.01. Additionally, the quality assessment of the fast-frozen sweet dumplings showed that those made with red adzuki bean mixed with glutinous rice flour (R-SD) had superior texture, reduced cracking, and less water loss compared to those made with GRF (G-SD), while maintaining similar color and odor to G-SD. The eGI value of 52.21 for R-SD also fell within the low eGI range, indicating its potential for developing low-eGI foods for patients with T2DM and other special populations.

Yeast Proteins: Proteomics, Extraction, Modification, Functional Characterization, and Structure: A Review.

Proteins are essential for human tissues and organs, and they require adequate intake for normal physiological functions. With a growing global population, protein demand rises annually. Traditional animal and plant protein sources rely heavily on land and water, making it difficult to meet the increasing demand. The high protein content of yeast and the complete range of amino acids in yeast proteins make it a high-quality source of supplemental protein. Screening of high-protein yeast strains using proteomics is essential to increase the value of yeast protein resources and to promote the yeast protein industry. However, current yeast extraction methods are mainly alkaline solubilization and acid precipitation; therefore, it is necessary to develop more efficient and environmentally friendly techniques. In addition, the functional properties of yeast proteins limit their application in the food industry. To improve these properties, methods must be selected to modify the secondary and tertiary structures of yeast proteins. This paper explores how proteomic analysis can be used to identify nutrient-rich yeast strains, compares the process of preparing yeast proteins, and investigates how modification methods affect the function and structure of yeast proteins. It provides a theoretical basis for solving the problem of inadequate protein intake in China and explores future prospects.

Ultrasound as Green Technology for the Valorization of Pumpkin Leaves: Intensification of Protein Recovery.

The recovery of valuable nutritional compounds, like proteins, from waste streams and by-products is a key strategy for enhancing production sustainability and opening up new market potential. This research aimed to use high-intensity ultrasound as an innovative technique to extract the soluble proteins from the pumpkin leaves. The impact of various sonication amplitudes and duration periods on protein yield, functional properties, antioxidant qualities, and structural characteristics, were studied. Utilization of ultrasound technology significantly increased the yield of pumpkin leaf protein by up to 40%-six times higher than maceration. The ultrasound extraction provided a RuBisCO-rich protein fraction with high radical scavenging and chelating activities, especially at 40% amplitude. Cavitation modified the tertiary and secondary structures of leaf proteins: the amount of α-helix changed based on amplitude (12.3-37.7%), the amount of random coil increased to 20.4%, and the amount of β-turn reduced from 31 to 18.6%. The alteration of the protein fluorescence spectrum (blue shift in spectrum) provides further evidence that ultrasound alters the proteins' molecular structure in comparation with maceration; the maximum tryptophan fluorescence intensity decreased from 22.000 to 17.096. The hydrophobicity values of 76.8-101.5 were substantially higher than the maceration value of 53.4, indicating that ultrasound improved the hydrophobicity of protein surfaces. Ultrasound resulted in a significant increase in solubility in an acidic environment with the increase in sonication amplitude. A 2.4-fold increase in solubility at pH 2 becomes apparent (20% amplitude; 43.1%) versus maceration (18.2%). The emulsifying ability decreases from 6.62 to 5.13 m2/g once the sonication amplitude increases by 20-70%. By combining the ultrasound periods and amplitudes, it is possible to create high-value protein leaf extracts with improved properties which can find real application as food additives and dietary supplements.

Protein glycosylation inhibitory effects and mechanisms of phloretin and phlorizin

The anti-glycation potential and mechanism of phloretin and phlorizin were investigated in the study. In the methylglyoxal (MGO)-human serum albumin (HSA) glycosylation system, the inhibition against fluorescent advanced glycosylation end products (AGEs) was more than 60% at 960 μM phloretin and phlorizin. They decreased carbonylation and oxidative damage of protein, protected thiol groups and secondary structure of protein and inhibited protein aggregates. Treated with 1.37 mM phloretin or phlorizin, O2−· scavenging was more than 80%, and 1 mM phloretin or phlorizin chelated 60.08% or 28.11% of Fe2+, respectively. Analysis of HPLC and LC-QqQ-MS shown phloretin captured MGO by forming adducts with MGO, with capture rates of 92.67% within 24 h. The capture rate of phlorizin to MGO was 56.40%. The anti-glycosylation mechanisms of them could include the structural protection of HSA, capture of MGO, O2−· and ·OH scavenging and chelation of Fe2+. These findings may provide a theoretical basis for the application of phloretin and phlorizin as novel anti-glycosylation agents.

Irradiation-induced modifications of apple seed protein isolate: Exploring techno-functional, structural, thermal, and morphological characteristics

Waste valorization of apple seeds for protein extraction is a sustainable approach to the management of apple seed waste in the apple processing industry. The purpose of the research is to study the modification of apple seed protein isolates under different doses of irradiation on functional, structural, thermal, and morphological characteristics. Different irradiation doses of 8, 15, 20 25, and 50 kGy showed significant variations in protein content (88.70%–86.45%), total phenolic content (774.13–285.42 mg GAE/100g), and color profile of the apple seed protein. Irradiation altered the apple seed protein isolates' functional properties with increased foaming properties and emulsifying properties and decreased water and oil absorption properties. Irradiation induces denaturation and cross-linking in the apple seed protein structures, which increase surface hydrophobicity (708.66–1740.66), decreased zeta potential (−18.60 to −39.39 mV), and alteration in protein secondary structures with decreased α-helix (11.52–10.43 %), β-sheet content (60.82–60.13%), and random coils (16.82–16.19%), and increased β turns (10.79–13.22 %). DSC and TGA analysis revealed improved thermal properties using irradiation doses of 8–20 kGy whereas reduction for 25–50 kGy in irradiated apple seed proteins. Scanning electronic microscopy showed pores and aggregated structures of irradiated apple seed protein isolates. The study revealed the potential of irradiation as one of the non-thermal techniques for modifying apple seed protein isolates for protein valorization in various food applications.

Effect of phosphorylated long‐chain inulin on the quality characteristics of fresh noodles

AbstractIn this paper, phosphorylation was employed to modify long‐chain inulin (PFXL) with the aim of improving the hydrophilicity and stability, thereby enhancing the nutritional value and quality of fresh wheat noodles. The textural characteristics, color, moisture distribution, and microstructure of the fresh noodles, as well as the secondary structure and disulfide bond content of gluten protein, were analyzed. The results indicate a significant enhancement in the quality of fresh noodles with the addition of PFXL. Specifically, the substitution of 6.0% PFXL for wheat flour yielded the highest springiness and whiteness in the fresh noodles. PFXL addition facilitated the transition of tightly bound water to weakly bound and free water within the noodle system, thereby contributing to the softness of the noodles. Furthermore, the introduction of 6% PFXL promoted the formation of a greater number of hydrogen and disulfide bonds, resulting in a higher content of α‐helix and β‐sheet structures. This collective effect served to enhance the overall quality of the noodles. These findings provide valuable insights into the potential applications of long‐chain inulin and offer compelling evidence for the production of high‐quality dietary fiber noodles.

Physico-functional properties, structural, and nutritional characterizations of Hodgsonia heteroclita oilseed cakes

The physicochemical and functional properties, structures, and nutritional characterizations of Hodgsonia heteroclita oilseed cake powder (OCP) obtained from oil extraction with no pretreatment (NP), heat pretreatment (HP; drying at 55 °C until reaching 10% moisture content), and the combined heat and enzymatic pretreatment (HEP; 2.98% (w/w) enzyme loading, 48 °C of incubation temperature and 76 min of incubation time) were investigated. HP and HEP caused a decrease in lightness but an increase in the yellow–brown color of OCP. The results showed that HEP-OCP had significantly lower oil and water absorption index, pasting properties and gelatinization enthalpy while higher water solubility index, foaming and emulsifying properties than NP-OCP and HP-OCP. Fourier transform infrared spectroscopy (FTIR) and X-ray diffraction indicated a small change in the protein secondary structure after pretreatment. Moreover, depending on pretreatment method, OCP samples contained a significant difference in nutritional values. However, all OCP samples could be claimed as high protein sources, containing all 9 essential amino acids and 9 non-essential amino acids. Finally, HEP-OCP seemed to have suitable properties to use as a potential ingredient in various food products such as soups, sauces, ice-cream, mousses, chiffon cakes and whipped toppings.

Ultrasound-assisted improvement of thawing quality of Tibetan pork by inhibiting oxidation

The challenge of meat quality degradation due to transportation difficulties in high-altitude plateaus underscores the importance of an efficient thawing process for Tibetan pork to ensure its quality. This study compared four thawing methods ultrasound thawing (UT), refrigerator thawing (RT), hydrostatic thawing (HT), and microwave thawing (MT) to assess their impact on the quality of Tibetan pork, focusing on thawing loss, tenderness, color variation, and alterations in protein secondary structure and moisture content. Additionally, the study examined the impact of thawing on the metabolites of Tibetan pork using metabolomics techniques. The results indicated that UT yielded the highest quality samples. UT significantly accelerated the thawing rate and had minimal impact on tenderness compared to traditional thawing methods. Moreover, protein and lipid oxidation levels were reduced by UT treatment. Furthermore, it enhanced the binding capacity of protein and water molecules, reduced drip loss, and maintained meat color stability. What’s more, amino acid metabolites such as l-glutamic acid, l-proline, oxidized glutathione, and 1-methylhistidine played a significant role in thawing oxidation in Tibetan pork, exhibiting a positive correlation with protein oxidation. UT resulted in a notable decrease in the levels of hypoxanthine and 2-aminomethylpyrimidine, contributing to the reduction of bitterness in the thawed meat and consequently enhancing the freshness of Tibetan pork. This study offers novel insights into understanding the biological changes occurring during the thawing process, while also furnishing a theoretical framework and technical assistance to improve the quality of Tibetan pork and propel advancements in food processing technology.