Number Of Amino Acid Residues Research Articles

Sodium Alginate–Soy Protein Isolate–Chitosan–Capsaicin–Nanosilver Multifunctional Antibacterial Composite Gel

We constructed a sodium alginate/soy protein isolate/chitosan gel system and incorporated silver nanoparticles reduced by capsaicin into the system, forming a sodium alginate–soy protein isolate–chitosan–capsaicin–silver nanoparticle composite gel (SA/SPI/CTS/CAP/Ag). In tests, the SA/SPI/CTS/CAP/Ag gel exhibited excellent antimicrobial properties. Using the agar diffusion method, the inhibition zone diameter for Staphylococcus aureus was determined to be 29.5 mm. Soy protein isolate (SPI), containing a large number of hydrophobic amino acid residues, effectively enhanced the moisture retention capability of the gel and improved its stability to a certain extent at an appropriate addition concentration. In a milk preservation experiment, the SA/SPI/CTS/CAP/Ag gel significantly extended the shelf-life of the milk. In dye adsorption experiments, the adsorption curve of the SA/SPI/CTS/CAP/Ag gel well fitted a pseudo-second-order kinetic model. It showed a degree of adsorption capacity for methylene blue, malachite green, methyl orange, and Congo red, with the most significant adsorption effect for malachite green being 42.48 mg/g. Considering its outstanding antimicrobial performance, preservation ability, and adsorption capacity, the SA/SPI/CTS/CAP/Ag gel holds significant potential in wastewater treatment and as an antimicrobial gel in the exploration of food preservation.

Genome-Wide Prediction and Expression Characterization of the GATA Gene Family under Nitrogen and Phosphate Deficiency in Panax ginseng

GATA transcription factors are widespread in plants, exerting crucial functions in multiple processes such as flower development, photoperiod regulation, and light signal transduction. The GATA gene family has a key role in the regulation of medicinal plant adaptation to environmental stress. However, since the publication of the Ginseng (Panax ginseng C.A. Meyer) genome-wide data, there has never been an analysis of the whole GATA gene family. To understand the function of the GATA gene family more broadly, the GATA gene family members in P. ginseng were predicted using an in silico bioinformatics approach. A comprehensive and systematic analysis encompassing chromosome scaffold, expression pattern, gene structure, and phylogeny was conducted. The results showed that a total of 52 GATA gene family members were recognized in P. ginseng, distributed across 51 scaffolds. Each member encoded a diverse number of amino acid residues, extending from 138 to 1064. Moreover, the expression levels of PgGATA genes were significantly altered by nitrogen (N) and phosphorus (P) stresses. The expression levels of PgGATA6, PgGATA11, PgGATA27, PgGATA32, PgGATA37, PgGATA39, PgGATA40, and PgGATA50 exhibited significant elevation under N deficiency, whereas PgGATA15, PgGATA18, PgGATA34, PgGATA38, PgGATA41, and PgGATA44 genes showed substantial upregulation under P deficiency. In addition, PgGATA3, PgGATA4, PgGATA14, PgGATA19, and PgGATA28 were substantially upregulated under both N and P deficiency. This research establishes a theoretical foundation for the thorough examination of the functions of the PgGATA gene family and its regulation by N and P fertilization during P. ginseng cultivation.

Risk mitigation strategy and mechanism analysis of neonicotinoid pesticides on earthworms

Neonicotinoid insecticides (NNIs) are a new class of widely used insecticides with certain risks to non-target organisms, like earthworms. The gray correlation method was used to calculate the comprehensive risk effect value of acute toxicity (LC50) and bioaccumulation (logKow) of NNIs on earthworms. A comprehensive effects three-dimensional quantitative structure–activity relationship (3D-QSAR) model was constructed, using NNIs molecular structures and the comprehensive effect value as the independent and dependent variables, respectively. One of the representatives guadipyr (GUA) was selected as the template molecule for the molecular design and modification. A total of 63 NNIs alternatives were designed with a reduced comprehensive value higher than 10%, and as high as 42%. After screening, 15 NNIs alternatives were screened with decreased acute toxicity to earthworms, bioaccumulation effects and improved functional property. The calculated primary acute risk quotient of earthworms shows that the designed NNIs alternatives have lower earthworm risks (reduction of 70.48–99.99%). Results also found that the electronic, geometric and topological parameters of NNIs are the key descriptors that affect NNIs alternatives' toxicity. The number of hydrophobic interaction amino acid residues in NNIs molecules also contributes to the acute toxicity and the bioaccumulation of NNIs alternatives on earthworms. This study aims to design and screen functionally improved and environmentally friendly NNIs alternatives that have low risk to earthworms and provide theoretical methods and new ideas for the risk control and development of pesticides represented by NNIs.

In silico study of properties in the series of 1-alkyl-4-(((5-nitrofuran-2-yl)methylene)amino)- 1,2,4-triazole halides

1,2,4-Triazole derivatives open up wide horizons for modern medicinal chemists to develop innovative drugs. The use of 1,2,4-triazole derivatives in pharmacological research is based on their ability to produce an effective effect on biological systems and interact with molecular targets. These azoles can be used to regulate various physiological processes, which opens up the possibility of their effective use in the treatment of various diseases. Targeted modification of the structure of 1,2,4-triazole derivatives opens up wide opportunities for the creation of biologically active compounds with improved properties, which contributes to further advances in pharmaceutical research and the development of new, effective drugs. The aim of this work is to predictively assess the pharmacological potential of 1-alkyl-4-(((5-nitrofuran-2-yl)methylene)amino)-1,2,4-triazole halides by in silico studies. Materials and methods. ADME-analysis is a method of studying the physical-chemical and pharmacokinetic parameters of the studied substances using the online resource SwissADME. Molecular docking is a method of predicting and evaluating the interaction between a ligand molecule and the three-dimensional structure of the target protein. The ligands have been prepared with the software MarvinSketch 6.3.0, Hyper Chem 8, and AutoDockTools-1.5.6, whereas the software packages Discovery Studio 4.0 and AutoDockTools-1.5.6 have been used for the preparation of enzymes. The Vina program was used for direct molecular docking. Results. A prescreening analysis was conducted on a virtual series of 1-alkyl-4-(((5-nitrofuran-2-yl)methylene)amino)-1,2,4-triazole halides, recognized as potential sources of biologically active substances. The study involved determining the main physicochemical characteristics and unveiling general pharmacokinetic parameters of the molecules. The Vina program was employed to identify the nature and number of amino acid residues in the active sites of model enzymes interacting with the proposed ligands. Results indicate the highest affinity for lanosterol 14α-demethylase. However, the analysis of ligand complexes with cyclooxygenase-2 and anaplastic lymphoma kinase suggests a low probability of a significant effect on these enzymes. Conclusions. The overall prognosis for bioavailability in the case of oral administration of dosage forms with the investigated substances is favorable. Pharmacodynamics in silico studies allow us to identify 1-heptyl- and 1-octyl-4-(((5-nitrofuran-2-yl)methylene)amino)-1,2,4-triazolium bromides as potential antifungal agents that can reasonably be involved in further in-depth studies of this type of activity.

Polyreactivity of antibodies from different B-cell subpopulations is determined by distinct sequence patterns of variable region.

An antibody molecule that can bind to multiple distinct antigens is defined as polyreactive. In the present study, we performed statistical analyses to assess sequence correlates of polyreactivity of >600 antibodies cloned from different B-cell types of healthy humans. The data revealed several sequence patterns of variable regions of heavy and light immunoglobulin chains that determine polyreactivity. The most prominent identified patterns were increased number of basic amino acid residues, reduced frequency of acidic residues, increased number of aromatic and hydrophobic residues, and longer length of CDR L1. Importantly, our study revealed that antibodies isolated from different B-cell populations used distinct sequence patterns (or combinations of them) for polyreactive antigen binding. Furthermore, we combined the data from sequence analyses with molecular modeling of selected polyreactive antibodies and demonstrated that human antibodies can use multiple pathways for achieving antigen-binding promiscuity. These data reconcile some contradictions in the literature regarding the determinants of antibody polyreactivity. Moreover, our study demonstrates that the mechanism of polyreactivity of antibodies evolves during immune response and might be tailored to specific functional properties of different B-cell compartments. Finally, these data can be of use for efforts in the development and engineering of therapeutic antibodies.

In silico evaluation of the pharmacodynamic component of the interaction of S-alkyl derivatives of 5-methyl-4-(p-tolyl)-1,2,4-triazole-3-thiol with some biological targets

Derivatives of 1,2,4-triazole open wide opportunities for modern and progressive scientists in the development of innovative medicines. These compounds are known for their variability and structural flexibility, which allows scientists to experiment and create new molecules with unique properties. The use of 1,2,4-triazole derivatives in the creation of drugs is based on their ability to interact with biological systems and molecular targets. These compounds can be aimed at regulating physiological processes, reducing manifestations of pathological conditions or enhancing necessary biological reactions. Directed modification of the structure of 1,2,4-triazole derivatives allows to create biologically active compounds with improved properties. The aim of the work was to study in silico and to evaluate the possible interaction of a virtual series of S-alkyl derivatives of 5-methyl-4-(p-tolyl)-1,2,4-triazole-3-thiol with some enzyme systems. Materials and methods. A computer method (molecular docking) for predicting and evaluating the interaction between a ligand molecule and a target protein structure. Ligand preparation was performed using MarvinSketch 6.3.0, Hyper Chem 8, and AutoDockTools-1.5.6 programs. Enzyme preparation involved the use of Discovery Studio 4.0 and AutoDockTools-1.5.6 software packages. Direct molecular docking was performed using the Vina program. Results. A virtual series of S-alkyl derivatives of 5-methyl-4-(p-tolyl)-1,2,4-triazole-3-thiol with the potential possibility of creating a biologically active substance has been constructed. Using the Vina software tool, the nature and number of amino acid residues of the active centers of model enzymes, with which the proposed ligands coordinate and bind, were determined. According to the results of docking studies, the predicted affinity for lanosterol-14α-demethylase was determined. The effect on the receptor tyrosine kinase of anaplastic lymphoma is somewhat inferior in terms of qualitative and quantitative indicators. Conclusions. Using the method of molecular docking, it was established that S-alkyl derivatives of 5-methyl-4-(p-tolyl)-1,2,4-triazole-3-thiol have a fairly significant potential for the manifestation of antifungal activity, which justifies the further synthesis of these compounds and more in-depth study of fungistatic and fungicidal properties. Docking results for anaplastic lymphoma kinase show little promise in the development of anticancer agents.

Structural analysis of open reading frames of bovine immunodeficiency virus proteins

The goal of this study was determining the structural organization peculiarities of the ORF2 and ORF3 proteins of the bovine immunodeficiency virus (BIV). Five ORFs were determined for two BIV isolates with complete genome using the ATGpr software, which permits effective prediction of translation initiation codons with nucleotide accuracy. Phyre2 software was used to predict, analyze the secondary structure and function of proteins. PONDR-FIT software was used to search for protein fragments in a disordered or natively unfolded state. Analysis of the amino acid composition of ORF2 and ORF3 proteins of BIVisolates regarding the presence of nonpolar, polar, aromatic, and hydrophobic amino acid residues was carried out using PSIPRED software. Models of the 3D-structure of proteins were obtained by I-TASSER server. 14% of α helices, 17% of β strands and 43% of disordered structure are predicted for the ORF3 protein. 37% of α helices, 0% of β strands, and 41% of disordered structure were determined for Gag polyprotein, which is translated from ORF2. The distribution of charged amino acid residues characterizes the surface properties of proteins. Their number reaches 23.9% for ORF2 protein. The amount of Arg is 5.2%, Lys — 8.0%, Glu — 7.3%, Asp — 3.4%. The total number of charged amino acid residues of ORF3 is 23.3%. The number of Arg is 12.6%, Lys — 4.9%, Glu — 1.9%, Asp — 3.9%. Only two ORFs of five ones coincide in nucleotide length (and, therefore, in length of corresponding proteins) for the two BIV isolates. The ORF3 protein belongs to the intrinsically disordered proteins that cannot be stably folded into a unique three-dimensional structure under physiological conditions, and the Gag polyprotein, which is translated from ORF2, belongs to the class of fully structured proteins. The secondary structure of both proteins shows the presence of α-helices

Characterization of swine hepatitis E virus genotype 3 open reading frames

The goal of this study was a determination of structural organization features of swine hepatitis E virus genotype 3 open reading frames. Gene selective pressure for genes was estimated using the Tajima’s neutrality test as implemented in MEGA 6. Shannon entropy was used for diversity detection at each position of open reading frames. Shannon entropy plots representing quantitative diversity at each amino acid (nucleotide) position of 11 swine HEV-3 isolates aligned sequences were calculated by software BioEdit. For phylogenetic analysis, nucleotide distances were analyzed using the neighbour-joining algorithm. Analysis of nucleotide, non-synonymous and synonymous distances was performed using MEGA6. Parameters of mutational analysis for swine hepatitis E virus genotype 3 open reading frames ORF1 – ORF3 were determined using Tajima’s neutrality test. Shannon entropy technique revealed that ORF3 is characterized by the most number of diverse amino acid residues (21,7 %) comparing with ORF1, ORF2 coding regions. Analysis of non-synonymous distances in ORF3 allowed to determine an order of evolutionary events in the history of swine HEV-3 isolates. Avian astroviruses strains were used as control because phylogenetic relationships among them correspond to the evolution history of their host species. Tree topology for swine HEV-3 ORF3 based on non-synonymous distances differs from tree structures based on nucleotide and synonymous distances. Positive values of D Tajima’s factor for ORF1, ORF2 of swine HEV-3 show on operating positive selection onto these coding regions. Negative value of D Tajima’s factor for ORF3 coding region indicates onto purifying selection

Evaluation of Linkers' Influence on Peptide-Based Piezoelectric Biosensors' Sensitivity to Aldehydes in the Gas Phase.

Recent findings qualified aldehydes as potential biomarkers for disease diagnosis. One of the possibilities is to use electrochemical biosensors in point-of-care (PoC), but these need further development to overcome some limitations. Currently, the primary goal is to enhance their metrological parameters in terms of sensitivity and selectivity. Previous findings indicate that peptide OBPP4 (KLLFDSLTDLKKKMSEC-NH2) is a promising candidate for further development of aldehyde-sensitive biosensors. To increase the affinity of a receptor layer to long-chain aldehydes, a structure stabilization of the peptide active site via the incorporation of different linkers was studied. Indeed, the incorporation of linkers improved sensitivity to and binding of aldehydes in comparison to that of the original peptide-based biosensor. The tendency to adopt disordered structures was diminished owing to the implementation of suitable linkers. Therefore, to improve the metrological characteristics of peptide-based piezoelectric biosensors, linkers were added at the C-terminus of OBPP4 peptide (KLLFDSLTDLKKKMSE-linker-C-NH2). Those linkers consist of proteinogenic amino acids from group one: glycine, L-proline, L-serine, and non proteinogenic amino acids from group two: β-alanine, 4-aminobutyric acid, and 6-aminohexanoic acid. Linkers were evaluated with in silico studies, followed by experimental verification. All studied linkers enhanced the detection of aldehydes in the gas phase. The highest difference in frequency (60 Hz, nonanal) was observed between original peptide-based biosensors and ones based on peptides modified with the GSGSGS linker. It allowed evaluation of the limit of detection for nonanal at the level of 2 ppm, which is nine times lower than that of the original peptide. The highest sensitivity values were also obtained for the GSGSGS linker: 0.3312, 0.4281, and 0.4676 Hz/ppm for pentanal, octanal, and nonanal, respectively. An order of magnitude increase in sensitivity was observed for the six linkers used. Generally, the linker's rigidity and the number of amino acid residues are much more essential for biosensors' metrological characteristics than the amino acid sequence itself. It was found that the longer the linkers, the better the effect on docking efficiency.

Study of molecular mechanisms of herbicide binding t o target proteins of weeds by in silico methods

The aim of this study was to study of the molecular mechanisms of herbicide binding (pinoxaden, quizalofop- P-tephuryl, prometryn, metribuzin, metsulfuron- methyl) to target proteins (acetyl- CoA carboxylase, acetolactate synthase, cytochrome P450, p-hydroxyphenylpyruvate dioxygenase) of the weed species growing in Siberia: wild oat Avena fatua (L.), wheatgrass Elymus repens (L.), amaranth Amaranthus retro exus (L.), common lamb's quarters Chenopodium album (L.), bristlegrass Setaria viridis (L.). The work was carried out in the Novosibirsk region in 2022-2023. Using bioinformatic methods, virtual three- dimensional complexes of pesticides and their targets were created. A new approach has been proposed to identify the parameters of the cavity of binding sites, which consists in combining the alignment method and machine learning technology. Docking of pesticides with targets was carried out. The calculation of the binding energy indicates a high degree of stability of the ligand- protein complexes. The in silico approach we proposed may be useful for elucidating the behavior of herbicides when bound to weed enzymes. This approach allows a deeper understanding of the mechanism of action and ecotoxicological aspects of the use of pesticides. The studied complexes of herbicides and proteins have a potential high stability due to the low binding energy with receptors, which varies from -5.60 to -13.24 kcal/mol. The binding energy value did not show a direct dependence on the number of amino acid residues of the ligand- binding site. In general, the study supplemented some aspects of the molecular mechanisms of binding herbicides to target proteins of weeds, however, a more in-depth study is required in order to localize critical amino acid points involved in the biological functions of target proteins.

Regulation of kisspeptin-54 activity of indolamine-2,3-dioxygenase and apoptosis of peripheral blood lymphocytes

Pregnancy is a phenomenon of natural semi-allogeneic transplantation, since the fetus is half alien due to the expression of paternal antigens. It was found that the hypothalamic hormone kisspeptin during pregnancy is produced by the syncytiotrophoblast of the placenta and participates in the formation of a new specific hormonal background. Several forms of the hormone circulate in the blood of pregnant women: kisspeptin-10, kisspeptin-14 and kisspeptin-54 (according to the number of amino acid residues in the hormone molecule), but the main active form is kisspeptin-54. The main mechanism for the formation of immune tolerance during pregnancy is the induction of the expression of the enzyme indolamine-2,3- dioxygenase (IDO) by antigen-presenting cells of peripheral blood, resulting in the catalysis of tryptophan (Trp) to kynurenins (KYN) blocking the activation and causing apoptosis of cytotoxic CD8+T lymphocytes in the zone of contact of maternal immune cells with placental-fetal complex antigens. In addition, during pregnancy, an important role is assigned to the process of apoptosis, since activated cells can be potentially dangerous for the developing fetus. Immunocompetent blood cells express a specific membrane receptor of kisspeptin (KISS-1R). Since kisspeptin-54 enters the systemic circulation only during pregnancy, the hormone has an effect on immune cells only during this period.The aim of this work was to evaluate the effect of kisspeptin-54 in concentrations comparable to its levelduring physiological pregnancy on IDO activity and apoptosis of peripheral blood lymphocytes.Peripheral blood mononuclear cells (PBMC) obtained from 10 healthy non-pregnant women of reproductive age (from 23 to 32 years) were used as the object of the study. Lymphocyte apoptosis was assessed in PBMC suspension by staining with annexin-V and propidium iodide. The determination of the number of cells in the early and late stages of apoptosis was carried out in the isolated gate of lymphocytes. IDO activity in PBMC was determined spectrophotometrically by changes in the concentration of KYN, the first stable metabolite of the Trp decay pathway.It was found that kisspeptin-54 at a concentration of 4.6 pM corresponding to the second trimester of pregnancy significantly enhances the activity of IDO, increases the number of cells in the early and late stages of apoptosis. Thus, kisspeptin-54 is an important mechanism for controlling these processes during pregnancy, aimed at protecting the semi-allogeneic fetus from adverse immune reactions of the mother and the favorable development of pregnancy.

Pulsed electric field improves the EGCG binding ability of pea protein isolate unraveled by multi-spectroscopy and computer simulation

Understanding molecular mechanisms during protein modification is critical for expanding the application of plant proteins. This study investigated the conformational change and molecular mechanism of pea protein isolate (PPI) under pulsed electric field (PEF)-assisted (-)-Epigallocatechin-Gallate (EGCG) modification. The flexibility of PPI was significantly enhanced after PEF treatment (10 kV/cm) with decrease (23.25 %) in α-helix and increase (117.25 %) in random coil. The binding constant and sites of PEF-treated PPI with EGCG were increased by 2.35 times and 10.00 % (308 K), respectively. Molecular docking verified that PEF-treated PPI had more binding sites with EGCG (from 4 to 10). The number of amino acid residues involved in hydrophobic interactions in PEF-treated PPI-EGCG increased from 5 to 13. PEF-treated PPI-EGCG showed a significantly increased antioxidant activity compared to non-PEF-treated group. This work revealed the molecular level of PEF-assisted EGCG modification of PPI, which will be significant for the application of PPI in food industry.

Cu+/Ag+ Competition in Type I Copper Proteins (T1Cu).

Due to the similarity in the basic coordination behavior of their mono-charged cations, silver biochemistry is known to be linked to that of copper in biological systems. Still, Cu+/2+ is an essential micronutrient in many organisms, while no known biological process requires silver. In human cells, copper regulation and trafficking is strictly controlled by complex systems including many cytosolic copper chaperones, whereas some bacteria exploit the so-called "blue copper" proteins. Therefore, evaluating the controlling factors of the competition between these two metal cations is of enormous interest. By employing the tools of computational chemistry, we aim to delineate the extent to which Ag+ might be able to compete with the endogenous copper in its Type I (T1Cu) proteins, and where and if, alternatively, it is handled uniquely. The effect of the surrounding media (dielectric constant) and the type, number, and composition of amino acid residues are taken into account when modelling the reactions in the present study. The obtained results clearly indicate the susceptibility of the T1Cu proteins to a silver attack due to the favorable composition and geometry of the metal-binding centers, along with the similarity between the Ag+/Cu+-containing structures. Furthermore, by exploring intriguing questions of both metals' coordination chemistry, an important background for understanding the metabolism and biotransformation of silver in organisms is provided.

Electronic structure calculations and deuterium NMR spectroscopy reveal retinal mobility in rhodopsin activation.

G-protein coupled receptors (GPCRs) regulate a number of physiological processes, where the visual receptor rhodopsin is an excellent prototype to investigate the structural fluctuations underlying GPCR function. Several X-ray crystal structures are available for the dark and active Meta-II states of rhodopsin. However, because of dehydrating conditions used to crystalize the protein, the conformation and orientation of the retinal chromophore in its binding pocket remain uncertain. Our hypothesis was that greater retinal mobility is needed in the active Meta-II state for the interaction with effector proteins. Accordingly, we investigated the structure and orientation of retinal in the dark and the Meta-II states using density functional theory (DFT) calculations and deuterium NMR (2H NMR) spectroscopy. For the computational simulations, we modeled the protein environment by including a number of amino acid residues in the retinal binding pocket and the water molecules around it. These models were tested with different chromophore orientations and protonation states of Glu113 and Glu181. Next, we performed DFT and complete active space (CAS) calculations to characterize the electronic structure of the dark and Meta-II states of rhodopsin. 2H NMR spectroscopic studies were also conducted on the active Meta-II state that contained deuterium-labelled retinal to experimentally validate the possible retinal orientations. The experiment revealed two possible retinal orientations (“flipped” and “unflipped”) without significant steric clashes in the binding pocket of active Meta-II state. By contrast, the DFT calculations show the Meta-II state predominantly contains the “flipped” orientation while the dark-state predominantly accommodates the “unflipped” retinal orientation. Thus the chromophore of the visual receptor undergoes significant mobility changes upon light activation of rhodopsin. [1] A.V. Struts et al. (2011) Nat.Struct.Mol.Biol. 18, 392–394, [2] M.N. Ryazantsev et al. (2019) J.Membr.Biol. 252, 425–449.

From bitter to delicious: properties and uses of microbial aminopeptidases.

Protein hydrolysates are easily digested and utilized by humans and animals, and are less likely to cause allergies. Protein hydrolysis caused by endopeptidases often leads to the exposure of hydrophobic amino acids at the ends of peptides, which consequently causes bitter taste. Microbial aminopeptidases remove the exposed hydrophobic amino acids at the ends of aminopeptides, which improves taste, allowing for easier production. This processe is attacking significant attention from industry and laboratories. Aminopeptidases selectively hydrolyze peptide bonds from the N-terminal of proteins or peptides to produce free amino acids. Aminopeptidases can be classified into leucine, lysine, methionine and proline aminopeptidases by hydrolyzed N-terminal residues; metallo-, serine- and cysteine- aminopeptidases by the reaction mechanisms; dipeptide and triphoptide enzymes by the released number of amino acid residues at the end of hydrolyzed peptides; or acidic, neutral and basic aminopeptidases by their optimal hydrolysis pH. Commercial aminopeptidases are generally produced by microbial fermentation, and are mainly applied in the debittering of protein hydrolysates, the deep hydrolysis of protein, and the production of condiments, cheese, and bioactive peptides, as well as for disease detection in the medical industry.

Functional diversity and plasticity in the sugar preferences of Saccharomyces MALT transporters in domesticated yeasts.

Maltose and maltotriose, together with glucose, are the major carbohydrates found in malts. Thus, brewing yeasts grown in malt-based brewing processes with serial re-pitching have likely increased their ability to uptake these sugars during domestication by modulating the expression and copy number of maltose transporter genes (MALT, also known as Malx1). However, the molecular basis for and structural insights into the sugar preferences of MALT proteins remain to be elucidated. Here we report the functional evaluation of two novel Saccharomyces cerevisiae MALT proteins, ScMalt#2p and ScMalt#5p, from industrial brewing yeasts, focusing on their maltose and maltotriose preferences. Structural models of the MALT proteins generated by AlphaFold2 and functional analyses of substitution mutants revealed that a very small number of amino acid residues in two spatially adjacent transmembrane helixes, TMH7 and TMH11, appear to be crucial for sugar preference. Thus, subtle conformational alterations conferred by a small number of amino acid polymorphisms within MALTs would contribute to the adaptation of domesticated brewing yeasts to the constrained carbohydrate environment of industrial wort during beer brewing.

Screening of xanthine oxidase inhibitory peptides by ligand fishing and molecular docking technology

Gout, as the second major metabolic disease after cardiovascular disease. Peptides have the advantages of natural and no side effects in the treatment and prevention of gout. This study aimed to screen xanthine oxidase (XOD) inhibitory peptides from Scophthalmus maximus protein as a drug basis for the treatment of gout. The specific results are as follows: Immobilization of xanthine oxidase 25.564 μg/mg by modified magnetic beads, and modified magnetic beads can be reused three times. Three decapeptides (FSLVHYAGTV, FTNEKLQQFF and WDDMEKIWHH) were screened, the IC50 were 3.741, 4.046 and 2.203 mg/mL. Circular dichroism and three-dimensional fluorescence spectra showed that the inhibitory peptide would change the helical structure of XOD and the internal hydrophobic environment. Molecular docking showed that the inhibitory effect of inhibitory peptides depends on the number of unique amino acid residues in the active center of XOD enzyme. In conclusion, this study provides a method for screening anti-gout peptides, which not only solves the problem of treating gout, but also realizes the high-value utilization of marine products. In addition, this method has substantial application value because of its low cost and simple operation.

Structural modeling, energetic analysis and molecular design of a π-stacking system at the complex interface of pediatric respiratory syncytial virus nucleocapsid with the C-terminal peptide of phosphoprotein

Human respiratory syncytial virus (RSV) is a primary cause of lower respiratory tract infections and hospital visits during infancy and childhood. The RSV phosphoprotein (P) is a major polymerase cofactor that interacts with nucleoprotein (N) to promote the recognition of ribonucleoprotein complex (RNP) by viral RNA polymerase. The binding pocket of N protein is chemically diverse, in or around which a number of aromatic and charged amino acid residues are observed. Previously, a nonapeptide segment (P peptide, 233DNDLSLEDF241) representing the C-terminal tail of P protein was identified to mediate the N-P interaction with a moderate affinity, in which the Phe241 at the end of P's C-terminus plays a critical role in the binding of P peptide to N protein. Here, we found that the side-chain aromatic phenyl moiety of P Phe241 residue can form short- and long-range cation-π interactions with N Arg132 and Arg150 residues, respectively, as well as T-shaped and parallel-displaced π-π stackings with N Tyr135 and His151 residues, respectively, which co-define a geometrically satisfactory π-stacking system at the complex interface of N protein with P peptide, thus largely stabilizing the complex architecture. The stacking effect was further optimized by systematically mutating the P Phe241 residue to other natural and non-natural aromatic amino acids with diverse chemical substitutions at the phenyl moiety to examine their structural and energetic effects on π-stacking system and on protein–peptide binding. The electron-donating mutations at the phenyl moiety of P Phe241 residue can effectively enhance the π-stacking system and then promote peptide binding, whereas the bulky and positively charged mutations would considerably impair the peptide potency by introducing steric hindrance and electrostatic repulsion. The [Tyr]P, [Thp]P and [Fph]P mutants were determined to have an increased affinity relative to wild-type P peptide, which could be used as self-inhibitory peptides to competitively disrupt the native interaction between N and P proteins.

Pathogenicity of Avian Polyomaviruses and Prospect of Vaccine Development.

Polyomaviruses are nonenveloped icosahedral viruses with a double-stranded circular DNA containing approximately 5000 bp and 5–6 open reading frames. In contrast to mammalian polyomaviruses (MPVs), avian polyomaviruses (APVs) exhibit high lethality and multipathogenicity, causing severe infections in birds without oncogenicity. APVs are classified into 10 major species: Adélie penguin polyomavirus, budgerigar fledgling disease virus, butcherbird polyomavirus, canary polyomavirus, cormorant polyomavirus, crow polyomavirus, Erythrura gouldiae polyomavirus, finch polyomavirus, goose hemorrhagic polyomavirus, and Hungarian finch polyomavirus under the genus Gammapolyomavirus. This paper briefly reviews the genomic structure and pathogenicity of the 10 species of APV and some of their differences in terms of virulence from MPVs. Each gene’s genomic size, number of amino acid residues encoding each gene, and key biologic functions are discussed. The rationale for APV classification from the Polyomavirdae family and phylogenetic analyses among the 10 APVs are also discussed. The clinical symptoms in birds caused by APV infection are summarized. Finally, the strategies for developing an effective vaccine containing essential epitopes for preventing virus infection in birds are discussed. We hope that more effective and safe vaccines with diverse protection will be developed in the future to solve or alleviate the problems of viral infection.

Interactions of Heavy Metals on Enzymes in Carbohydrate Metabolism: In silico study on glucokinase and pyruvate kinase

Cadmium (Cd2+) and mercury (Hg2+) are heavy metals, which can cause chronic inflammation, oxidative stress, obesity, hyperglycemia, and diabetes. Exposure to heavy metals cadmium and mercury can interfere with glycolysis metabolic functions through the inactivation of two key enzymes: glucokinase (GK) and pyruvate kinase (PyK). However, pathomechanism is unknown. Based on the background, this research was conducted. Enzyme structures were obtained from the RCSB Protein Data Bank (http://www.rcsb.org) with the following codes, GK (GDP ID: 3IDH) and PyK (GDP ID: 4IP7). The interaction between Cd and Hg with this enzyme was used via the MIB site: Metal Ion Binding site prediction and docking server (http://bioinfo.cmu.edu.tw/MIB/). Next, the target protein's interaction between metal ions and amino acids was visualized on UCSF Chimera 1.15. Based on the research results, the metal ion bond of mercury was more reactive than cadmium based on the number of amino acid residues bound. The bond was stronger based on a lower distance with PyK and GK enzymes. Therefore, mercury and cadmium metal ions were considered to inhibit the glycolysis process by causing the inactivation of the two enzymes.