Physicochemical Properties and Biological Activities of Silver Carp Scale Peptide and Its Nanofiltration Fractions

To explore the physicochemical properties and biological functions of silver carp scale peptide (SCSP), its molecular-weight fractions SCSP-I, II, and III obtained by nanofiltration were assessed for their solubility, emulsibility, free radical scavenging ability, effect on the proliferation of mouse B16 cells. The results showed that the solubility of each fraction of SCSP was higher than 90%, SCSP-II and III were higher than 95%. The antioxidant powers on ⦁OH, O2-⦁ and Fe3+ were ranked as SCSP-III > SCSP-II > SCSP-I > SCSP. All fractions of SCSP had no toxic or side effects in mouse B16 melanoma cells experiments in vitro. At a concentration of 0.01 mg/mL, the tyrosinase activity of B16 cells in the SCSP-II fraction was significantly lower than that of the α-arbutin (P < 0.05), at 65.37%. The molecular weight distribution of SCSP was 399–1404 Dalton and 13 peptide sequences were detected. Among them, SCSP-II contained many hydrophobic amino acids, and SCSP-III stood out for combining arginine with hydrophobic amino acids. This may be the reason why the low molecular-weight SCSPs show the strong antioxidant activity and strong tyrosinase inhibition. The work provides a data base for the development of SCSP and increases the possibility of its application.

Improvement of Functional Properties of Jack Bean (Canavalia ensiformis) Flour by Germination and Its Relation to Amino Acids Profile

Jack bean as a source of vegetable protein had not been popular. Seed germination had been known to improve its nutritional quality, especially protein and amino acid profile. This study determined the effect of germination on the color, beany flavor, protein content, functional properties, and amino acid profile of jack bean flour. A complete randomized design was used for this experiment. Germination was carried out for 0, 24, 48, and 72 hours. The seed (control) and germinated jack bean flours were analyzed for oil absorption, water absorption, emulsifying and foaming capacities, as well as the soluble protein content to determine the best germination time. Furthermore, the amino acid profile of the jack bean flour produced from the best germination time was analyzed. The results of this study indicated that the total and soluble protein of the seed and germinated jack bean seeds for 0, 24, 48, 60, and 72 hours were 23.30 and 5.95; 22.61 and 7.61; 21.18 and 10.68; 23.26 and 10.22; 23.98 and 10.81%, respectively. Germination of jack bean improved the functional properties. A germination time of 72 hours increased the oil capacity, water absorption capacity, foaming capacity and decreased the emulsion capacity significantly. The hydrophilic and hydrophobic amino acids of the germinated jack bean flour increased to 3.21 and 2.12% of the seed flour, respectively. The increase of the foaming capacity was related to the increase in hydrophobic amino acids of germinated jack bean flour compared to seed flours, that were glycine 1.23 and 1.01; alanine 1.29 and 1.01; valine 1.16 and 1.00; leucine 1.84 and 1.09%, respectively. Germination of jack bean for 72 hours increased significantly the essential amino acids, namely: leucine, lysine, and valine.

Omicron and Delta Variant of SARS-CoV-2: A Comparative Computational Study of Spike protein

Emerging SARS-CoV-2 variants, especially those of concern, may have an impact on the virus’s transmissibility and pathogenicity, as well as diagnostic equipment performance and vaccine effectiveness. Even though the SARS-CoV-2 Delta variant (B.1.617.2) emerged during India’s second wave of infections, Delta variants have grown dominant internationally and are still evolving. On November 26, 2021, WHO identified the variant B.1.1.529 as a variant of concern, naming it Omicron, based on evidence that Omicron contains numerous mutations that may influence its behaviour. However, the mode of transmission and severity of the Omicron variant remains unknown. We used computational studies to examine the Delta and Omicron variants in this work and found that the Omicron variant had a higher affinity for human ACE2 than the Delta variant due to a significant number of mutations in the SARS-CoV-2 receptor binding domain, indicating a higher potential for transmission. Based on docking studies, the Q493R, N501Y, S371L, S373P, S375F, Q498R, and T478K mutations contribute significantly to high binding affinity with human ACE2. In comparison to the Delta variant, both the entire spike protein and the RBD in Omicron include a high proportion of hydrophobic amino acids such as leucine and phenylalanine. These amino acids are located within the protein’s core and are required for structural stability. Omicron has a higher percentage of alpha-helix structure than the Delta variant in both whole spike protein and RBD, indicating that it has a more stable structure. We observed a disorder-order transition in the Omicron variant between spike protein RBD regions 468-473, and it may be significant in the influence of disordered residues/regions on spike protein stability and binding to ACE2. A future study might investigate the epidemiological and biological consequences of the Omicron variant.

Comparing Native Crystal Structures and AlphaFold2 Predicted Water-Soluble G Protein-Coupled Receptor QTY Variants

Accurate predictions of 3-dimensional protein structures by AlphaFold2 is a game-changer for biology, especially for structural biology. Here we present the studies of several native chemokine receptors including CCR5, CCR9, CXCR2 and CXCR4 determined by X-ray crystallography, and their water-soluble QTY counter parts predicted by AlphaFold2. In the native structures, there are hydrophobic amino acids leucine (L), isoleucine (I), valine (V) and phenylalanine (F) in the transmembrane helices. These hydrophobic amino acids are systematically replaced by hydrophilic amino acids glutamine (Q), threonine (T), and tyrosine (Y). Thus, the QTY variants become water-soluble. We also present the superimposed structures of native CCR10, CXCR5, CXCR7 and an olfactory receptor OR1D2 and their water-soluble QTY variants. Since the CryoEM structural determinations for the QTY variants of CCR10QTY and OR1D2QTY are in progress, it will be of interest to compare them when the structures become available. The superimposed structures show remarkable similarity within RMSD 1Å–2Å despite significant sequence differences (~26%–~33%). We also show the differences of hydrophobicity patches between the native GPCR and their QTY variants. Our study provides insight into the subtle differences between the hydrophobic helices and hydrophilic helices, and may further stimulate designs of water-soluble membrane proteins and other aggregated proteins.

The role vegetable proteins to stabilize emulsion: a mini review

The critical aspect in forming emulsion is the selection of the right emulsifier. Emulsifiers are facilitating emulsion formation and promoting emulsion stability. Protein is the emulsifier that is often found in the food industry, because it has an active surface containing a mixture of hydrophilic and hydrophobic amino acids along the polypeptide chains. Protein have emulsification properties due to their amphipathic properties (having hydrophobic and hydrophilic groups) are the properties of proteins as emulsification because these proteins are able to form a layer at the oil-water interface. However, protein-stabilized emulsions are sensitive to charge changes, and proteins tend to diffuse slowly towards the interface compared to emulsifiers with smaller molecular weight. The purpose of this literature review is to determine the ability of vegetable proteins to stabilize emulsions.

Amino Acid Dependent Performance of Modified Chitosan Against Bacteria and Red Blood Cell

In order to combat antibiotic resistance, the development of new antibacterial agents is essential. In this study, we prepared four types of amino acid modified chitosan (CS-AA). Compared with chitosan modified with hydrophobic amino acids, the chitosan modified with positively charged amino acids showed higher antibacterial efficiency against Escherichia coli (E. coli) under similar grafting rate. CS-AA achieves antibacterial properties mainly by destroying the integrity of bacterial cell membranes. All the four types of CS-AA show low toxicity towards red blood cells. This work indicates that positively charged groups are more important than hydrophobic groups in the design of chitosan-based antibacterial agents, and provides helpful information for the molecular design of effective antibacterial agents.

Synthesis and Inhibition Activity Study of Triazinyl-Substituted Amino(alkyl)-benzenesulfonamide Conjugates with Polar and Hydrophobic Amino Acids as Inhibitors of Human Carbonic Anhydrases I, II, IV, IX, and XII

Primary sulfonamide derivatives with various heterocycles represent the most widespread group of potential human carbonic anhydrase (hCA) inhibitors with high affinity and selectivity towards specific isozymes from the hCA family. In this work, new 4-aminomethyl- and aminoethyl-benzenesulfonamide derivatives with 1,3,5-triazine disubstituted with a pair of identical amino acids, possessing a polar (Ser, Thr, Asn, Gln) and non-polar (Ala, Tyr, Trp) side chain, have been synthesized. The optimized synthetic, purification, and isolation procedures provided several pronounced benefits such as a short reaction time (in sodium bicarbonate aqueous medium), satisfactory yields for the majority of new products (20.6–91.8%, average 60.4%), an effective, well defined semi-preparative RP-C18 liquid chromatography (LC) isolation of desired products with a high purity (>97%), as well as preservation of green chemistry principles. These newly synthesized conjugates, plus their 4-aminobenzenesulfonamide analogues prepared previously, have been investigated in in vitro inhibition studies towards hCA I, II, IV and tumor-associated isozymes IX and XII. The experimental results revealed the strongest inhibition of hCA XII with low nanomolar inhibitory constants (Kis) for the derivatives with amino acids possessing non-polar side chains (7.5–9.6 nM). Various derivatives were also promising for some other isozymes.

Transcriptional repressor Gal80 recruits corepressor complex Cyc8–Tup1 to structural genes of the Saccharomyces cerevisiae GAL regulon

Under non-inducing conditions (absence of galactose), yeast structural genes of the GAL regulon are repressed by Gal80, preventing interaction of Gal4 bound to UASGAL promoter motifs with general factors of the transcriptional machinery. In this work, we show that Gal80 is also able to interact with histone deacetylase-recruiting corepressor proteins Cyc8 and Tup1, indicating an additional mechanism of gene repression. This is supported by our demonstration that a lexA–Gal80 fusion efficiently mediates repression of a reporter gene with an upstream lexA operator sequence. Corepressor interaction and in vivo gene repression could be mapped to a Gal80 minimal domain of 65 amino acids (aa 81-145). Site-directed mutagenesis of selected residues within this domain showed that a cluster of aromatic-hydrophobic amino acids (YLFV, aa 118-121) is important, although not solely responsible, for gene repression. Using chromatin immunoprecipitation, Cyc8 and Tup1 were shown to be present at the GAL1 promoter in a wild-type strain but not in a gal80 mutant strain under non-inducing (derepressing) growth conditions. Expression of a GAL1–lacZ fusion was elevated in a tup1 mutant (but not in a cyc8 mutant) grown in derepressing medium, indicating that Tup1 may be mainly responsible for this second mechanism of Gal80-dependent gene repression.