Chain Amino Acids Research Articles

Bioactive Peptides from Fermented Foods: Production Approaches, Sources, and Potential Health Benefits.

Microbial fermentation is a well-known strategy for enhancing the nutraceutical attributes of foods. Among the fermentation outcomes, bioactive peptides (BAPs), short chains of amino acids resulting from proteolytic activity, are emerging as promising components thanks to their bioactivities. Indeed, BAPs offer numerous health benefits, including antimicrobial, antioxidant, antihypertensive, and anti-inflammatory properties. This review focuses on the production of bioactive peptides during the fermentation process, emphasizing how different microbial strains and fermentation conditions influence the quantity and quality of these peptides. Furthermore, it examines the health benefits of BAPs from fermented foods, highlighting their potential in disease prevention and overall health promotion. Additionally, this review addresses the challenges and future directions in this field. This comprehensive overview underscores the promise of fermented foods as sustainable and potent sources of bioactive peptides, with significant implications for developing functional foods and nutraceuticals.

Conductance Channels in a Single-Entity Enzyme.

For a long time, the prevailing view in the scientific community was that proteins, being complex macromolecules composed of amino acid chains linked by peptide bonds, adopt folded structure with insulating or semiconducting properties, with high bandgaps. However, recent discoveries of unexpectedly high conductance levels, reaching values in the range of dozens of nanosiemens (nS) in proteins, have challenged this conventional understanding. In this study, we used scanning tunneling microscopy (STM) to explore the single-entity conductance properties of enzymatic channels, focusing on bilirubin oxidase (BOD) as a model metalloprotein. By immobilizing BOD on a conductive carbon surface, we discern its preferred orientation, facilitating the formation of electronic and ionic channels. These channels show efficient electron transport (ETp), with apparent conductance up to the 15 nS range. Notably, these conductance pathways are localized, minimizing electron transport barriers due to solvents and ions, underscoring BOD's redox versatility. Furthermore, electron transfer (ET) within the BOD occurs via preferential pathways. The alignment of the conductance channels with hydrophilicity maps, molecular vacancies, and regions accessible to electrolytes explains the observed conductance values. Additionally, BOD exhibits redox activity, with its active center playing a critical role in the ETp process. These findings significantly advance our understanding of the intricate mechanisms that govern ETp processes in proteins, offering new insights into the conductance of metalloproteins.

Anti-Obesity Effects of a Collagen with Low Digestibility and High Swelling Capacity: A Human Randomized Control Trial

Background/Objectives: Collagen is a protein formed by very long amino acid chains. When conveniently treated, it can incorporate water into the net, thus increasing its volume and mass. The present work aimed to evaluate the potential anti-obesity effects of bovine collagen that has been technologically treated to increase its water retention capacity in an acid pH medium, with the objective of inducing satiation. Methods: Collagen’s digestibility was tested with a pepsin digestion test. Its swelling capacity was tested in an acid pH medium simulating gastric conditions. Postprandial levels of ghrelin in response to collagen supplementation were tested in rats. In a randomized control trial, 64 subjects with overweight/obesity were allocated in two groups: supplemented daily with two protein bars enriched with collagen (20 g per day) for 12 weeks, or control group. Anthropometric and biochemical measurements were assessed in all the participants. Results: This collagen showed a low digestibility (<60%) and high swelling capacity (>1900%) in vitro. In humans with overweight and obesity, this collagen significantly reduced body weight, body mass index (BMI), systolic blood pressure (SBP), and fatty liver index (FLI) and increased fat-free mass when compared with the control group. A significant reduction in the sarcopenic index; total, troncular, and visceral fat (measured by DEXA); and serum leptin levels were observed in the collagen group at the end of the intervention, with no differences with respect to controls. Collagen reduced the sensation of hunger and increased fullness and satisfaction. In male Wistar rats, collagen decreased postprandial blood ghrelin levels. Conclusions: Collagen supplementation (20 g per day for 12 weeks) reduced body weight, BMI, waist circumference, fat mass, FLI, and SBP in humans with overweight and obesity, which might be related to the increased sensation of fullness and satisfaction reported by the volunteers after the intake.

Changes in Texture and Collagen Properties of Pork Skin during Salt-Enzyme-Alkali Tenderization Treatment.

The effects of salt-enzyme-alkali progressive tenderization treatments on porcine cortical conformation and collagen properties were investigated, and their effectiveness and mechanisms were analyzed. The tenderization treatment comprised three treatment stages: CaCl2 (25 °C/0-30 min), papain (35 °C/30-78 min), and Na2CO3 (25 °C/78-120 min). The textural, microscopic, and collagenous properties (content, solubility, and structure) of pork skin were determined at the 0th, 30th, 60th, 90th, and 120th min of the treatment process. The results showed that the shear force, hardness, and chewability of the skin decreased significantly (p < 0.05), and the elasticity exhibited a gradual increase with the progression of tenderization. The content and solubility of collagen showed no significant change at the CaCl2 treatment stage. However, the soluble collagen content increased, the insoluble collagen content decreased, and the collagen solubility increased by 18.04% during the subsequent treatment with papain and Na2CO3. Meanwhile, the scanning electron microscopy results revealed that the regular, wavy structure of the pig skin collagen fibers gradually disappeared during the CaCl2 treatment stage, the overall structure revealed expansion, and the surface microscopic pores gradually increased during the papain and Na2CO3 treatment stages. The findings of the Fourier transform infrared spectroscopy analysis indicated that the hydrogen bonding interactions between the collagen molecules and the C=O, N-H and C-N bonds in the subunit structure of collagen were substantially altered during treatment and that the breakage of amino acid chains and reduction in structural ordering became more pronounced with prolonged treatment. In the tertiary structure, the maximum emission wavelength was blue-shifted and then red-shifted, and the fluorescence intensity was gradually weakened. The surface hydrophobicity was slowly increased. The salt-enzyme-alkali tenderization treatment considerably improved the physical properties and texture of edible pork skins by dissolving collagen fibers and destroying the structure of collagen and its interaction force.

The evolution of amino acids under asteroidal aqueous alteration

Carbonaceous chondrites contain amino acids, with variable abundances and isotope compositions between and within carbonaceous chondrites. The parent body processes, and the presence of clay minerals may explain those differences. Here, we experimentally investigate the evolution of 6 amino acids (glycine, β-alanine, α-alanine, 2-aminoisobutyric acid, γ-aminobutyric acid, and isovaline) exposed to hydrothermal conditions in the presence or absence of silicates. We determined the chemical nature and isotopic composition of the organic compounds of the soluble and solid fractions of the residues using X-ray diffraction, spectroscopy, and mass-spectrometry methods. Glycine and α-alanine exhibit a rather high stability, which is consistent with the measured abundances of α-alanine and glycine in chondrites having experienced various degrees of aqueous alteration. In the meantime, the evolution of β-alanine under hydrothermal conditions leads to the formation of a new compound, which likely results from the decarboxylation and deamination of β-alanine followed by recombination. More than 95 % of γ-ABA was transformed into 2-pyrrolidione though self-cyclization during the aqueous alteration. The solid residues of the experiments conducted in the presence of clay minerals contain organic material, with abundances varying depending on the amino acid used for the experiments (TOC isovaline > 2-aminoisobutyric acid > γ-aminobutyric acid > glycine > α-alanine > β-alanine). Clay minerals thus preferentially trap branched amino acids over chained amino acids, likely within their interlayer spaces as suggested by XRD data. The δ13C values of amino acids have not changed significantly during the experiments, even with the presence of silicates. Thus, the δ13C values of amino acids reported in CR and CM chondrites likely relate to synthetic conditions or the origin of their precursors (i.e. inherited from the pre-accretion processes).

Hemoglobin targeting potential of aminocarb pesticide: Investigation into dynamics, conformational stability, and energetics in solvent environment

Aminocarb (AMC), a carbamate pesticide, due to its prevalent usage exhibits increased accumulation in the environment affecting both insects and humans. It enters the human body via food grains and be transported through bloodstream. AMC's chemical structure, containing specific molecular frameworks and functional groups, enables it to bind with proteins like albumin and hemoglobin. Given that molecules with similar architecture are known to bind with hemoglobin, we aimed to explore Aminocarb's binding capability and the potential mechanism or mode of its interaction with hemoglobin. Hb being a tetramer with a profound interface between amino acid chains offers multiple binding sites. It is therefore important to investigate the structural aspects of binding of AMC by employing various spectroscopic and in-silico methods. The surface of the α1 chain near the α1β2 interface emerges as the preferred binding site for AMC, primarily due to its conformational restrictions. In its bound state, AMC tends to maintain a relaxed conformation, closely resembling its globally optimized geometry, and resides in close proximity to the α1 chain via multiple hydrophobic contacts and water bridge as observed in molecular dynamics (MD) simulations. Fluorescence quenching experiments showed moderate binding strength (7.7 × 10⁴ L M⁻1 at 288 K, 7.8 × 10⁴ L M⁻1 at 298 K, 7.9 × 10⁴ L M⁻1 at 308 K) and spontaneous binding, driven by hydrophobic and van der Waals interactions, as indicated by enthalpy (0.80–0.91 kJ mol⁻1), entropy (0.0970–0.0974 kJ mol⁻1), and Gibbs free energy (−27.13 to - 29.08 kJ mol⁻1). Circular dichroism experiments reveal no major structural changes in Hb. Quantum chemical calculations and MD simulations reveal conformation-dependent energy differences, enhancing our understanding of AMC's binding mechanism to Hb.

Synthesis, spectroscopy, solvation effect, topology and molecular docking studies on 2,2′-((1,2 phenylenebis (azaneylylidene)) bis (methaneylylidene)) bis(4-bromophenol)

The 2,2′-((1,2 phenylenebis (azaneylylidene)) bis (methaneylylidene)) bis(4-bromophenol) (5BSOP) Schiff base was synthesized, characterized using different spectroscopic techniques, and the data are compared with predictions from DFT computations. The calculated energy values are -8.65 eV (HOMO) and -6.66 eV (LUMO), and the energy gap was found to be 1.99 eV. The reactive atom sites in the chemical are identified by MEP analysis. The locations of localized and delocalized orbitals are revealed through ELF and LOL surface maps. The sites of non-covalent interactions are exposed by RDG and NCI analysis. The possible inter and intra-molecular interactions were determined by NBO analysis and the highest stabilization energy observed was 40.07 kcal/mol. Biological performance as a HMGCS2 expression enhancer was predicted by Pass online studies. Molecular docking simulation with protein 706I having HMGCS2 expression inhibition characteristics revealed a stable receptor-ligand interaction pose at a binding energy of -4.74 kcal/mol. The interaction of the Phe61 amino acid chain of 706I with 5BSOP through conventional H-bond expressed a bond distance of 3.24 A°.

N-terminal domain of androgen receptor is a major therapeutic barrier and potential pharmacological target for treating castration resistant prostate cancer: a comprehensive review.

The incidence rate of prostate cancer (PCa) has risen by 3% per year from 2014 through 2019 in the United States. An estimated 34,700 people will die from PCa in 2023, corresponding to 95 deaths per day. Castration resistant prostate cancer (CRPC) is the leading cause of deaths among men with PCa. Androgen receptor (AR) plays a critical role in the development of CRPC. N-terminal domain (NTD) is the essential functional domain for AR transcriptional activation, in which modular activation function-1 (AF-1) is important for gene regulation and protein interactions. Over last 2decades drug discovery against NTD has attracted interest for CRPC treatment. However, NTD is an intrinsically disordered domain without stable three-dimensional structure, which has so far hampered the development of drugs targeting this highly dynamic structure. Employing high throughput cell-based assays, small-molecule NTD inhibitors exhibit a variety of unexpected properties, ranging from specific binding to NTD, blocking AR transactivation, and suppressing oncogenic proliferation, which prompts its evaluation in clinical trials. Furthermore, molecular dynamics simulations reveal that compounds can induce the formation of collapsed helical states. Nevertheless, our knowledge of NTD structure has been limited to the primary sequence of amino acid chain and a few secondary structure motif, acting as a barrier for computational and pharmaceutical analysis to decipher dynamic conformation and drug-target interaction. In this review, we provide an overview on the sequence-structure-function relationships of NTD, including the polymorphism of mono-amino acid repeats, functional elements for transcription regulation, and modeled tertiary structure of NTD. Moreover, we summarize the activities and therapeutic potential of current NTD-targeting inhibitors and outline different experimental methods contributing to screening novel compounds. Finally, we discuss current directions for structure-based drug design and potential breakthroughs for exploring pharmacological motifs and pockets in NTD, which could contribute to the discovery of new NTD inhibitors.

Sub-nanometer size level regulation of biomimetic channels in porous membrane for high-capacity removal of toxic dye contaminants

Organic dyes are an important chemical with a market demand of millions of tons. However, their massive emissions, especially alkaline dye contaminants, have caused serious disruption of the ecosystem and even cancers. Inspired by bionic mass transfer, several amino acid fragments (carboxylic acid, γ-aminobutyric acid, and glutamic acid) are introduced into the 2.5 nm-pore size cavity through in-situ polymerization. The flexible amino acid chains facilitate the transport of guest molecules into the channels, accelerating their movement within the porous framework. These flexible chains are implanted into a 2.5 nm pore cavity, forming a 0.8–1.5 nano-meter-sized confinement space, bringing about the strong absorption capability for alkaline contaminants. Notably, LNU-74-glutamic acid achieves an ultra-fast absorption rate for toxic dye contaminants (4.74 g g−1h−1), as well as the highest capacity per unit area among all reported porous adsorbents, including porous carbons, metal–organic frameworks, porous polymers. After encapsulation in commercial polymer, the mixed-matrix membrane reveals (LNU-74-glutamic acid@MMM) a rejection rate greater than 98 % in various real water environments at permeation flux of ∼320 L m−2h−1, including strong acid/alkali, river water, and seawater.

Low-temperature plasma jet treatment generates reactive oxygen species in solution that leads to peptide oxidation and protein aggregation

Abstract Low-temperature plasma (LTPs) jets are FDA-approved medical devices to remove cancerous tissue and aid in wound healing. However, reports on their reaction with proteins are conflicting, ranging from fragmentation, oxidation, aggregation, or a combination thereof. In this study we bridge the gap between plasma-treatment of short peptides to proteins at physiologically relevant concentrations. The LTP in this study is based on a helium dielectric barrier discharge (DBD) that forms a plasma-jet, which is directed at the solution without direct contact with the plasma, and results in the formation of reactive oxygen species (ROS) OH• and O2•- in solution. The longer the solution is treated, the more solution-phase ROS form. Treating peptide- and protein-containing solutions leads to extensive oxidation. The ROS led to the same oxidative modifications for peptide M with increasing chain length (9, 18, 37, 76 amino acids), which could be identified with high-resolution mass spectrometry. Oxidized species M+xO led to conformational changes such as compaction and elongation, while the unmodified peptide M remained unaltered, as found by ion mobility spectrometry and size exclusion chromatography. For proteins at high concentration, insoluble aggregates formed and could be identified by UV/Vis light scattering and atomic force microscopy. The formation of aggregates is dependent on the amino acid chain length, the peptide concentration, and the time for aggregate formation. These findings highlight the importance of both peptide chain length and concentration in determining the fate of peptides following the exposure to LTP, while also offering valuable insights for the field of plasma medicine. &amp;#xD;

Hybrid Diffusion Model for Stable, Affinity-Driven, Receptor-Aware Peptide Generation.

The convergence of biotechnology and artificial intelligence has the potential to transform drug development, especially in the field of therapeutic peptide design. Peptides are short chains of amino acids with diverse therapeutic applications that offer several advantages over small molecular drugs, such as targeted therapy and minimal side effects. However, limited oral bioavailability and enzymatic degradation have limited their effectiveness. With advances in deep learning techniques, innovative approaches to peptide design have become possible. In this work, we demonstrate HYDRA, a hybrid deep learning approach that leverages the distribution modeling capabilities of a diffusion model and combines it with a binding affinity maximization algorithm that can be used for de novo design of peptide binders for various target receptors. As an application, we have used our approach to design therapeutic peptides targeting proteins expressed by Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) genes. The ability of HYDRA to generate peptides conditioned on the target receptor's binding sites makes it a promising approach for developing effective therapies for malaria and other diseases.

Toxicity of antimony to plants: Effects on metabolism of N and S in a rice plant

Excess antimony (Sb) has been shown to damage plant growth. Rice plants readily absorb a large amount of Sb after a long period of flooding, yet the mechanisms underlying Sb toxicity in plants have not been solved. This study was conducted to explore the effects of Sb on the uptake of N and S, and monitor the concentrations of reduced glutathione (GSH) and enzymes associated with these processes. In addition, we analyzed differentially expressed metabolites (DEMs) correlated with amino acids (AAs) and oligopeptides, specifically DEMs containing sulfur (S), GSH and indole–3–acetic acid (IAA). The results showed that antimonite [Sb(III)] inhibited shoot growth whereas antimonate [Sb(V)] stimulated shoot growth. Interestingly, Sb(III)5/10 enhanced shoot concentrations of total nitrogen (N), NH4+–N [only at Sb(III)10] and S; but reduced the shoot concentrations of NO3–N and soluble protein. Sb(III)5/10 addition significantly increased oxidized glutathione (GSSG) concentration and activities of glutathione peroxidase (GSH–Px) and glutathione S-transferase (GST) but non–significantly affected concentration of reduced glutathione (GSH) and activities of γ-glutamylcysteine synthetase (GCL) and glutathione reductase (GR), suggesting Sb(III) restricted GSH recycling. Addition of Sb (1) increased the abundance of DEMs associated with lignins, Ca uptake, toxicity/detoxification, and branched chain AAs; (2) decreased the abundance of AAs inclcuding isoleucine (Ile), leucine (Leu), tryptophan (Trp), tyrosine (Tyr) and histidine (His); (3) increased the abundance of arginine (Arg), putrescine (Put) and spermidine (Spd); and (4) affected methylation and acetylation of many AAs, especially acetylation.

ACP-ESM: A novel framework for classification of anticancer peptides using protein-oriented transformer approach

Anticancer peptides (ACPs) are a class of molecules that have gained significant attention in the field of cancer research and therapy. ACPs are short chains of amino acids, the building blocks of proteins, and they possess the ability to selectively target and kill cancer cells. One of the key advantages of ACPs is their ability to selectively target cancer cells while sparing healthy cells to a greater extent. This selectivity is often attributed to differences in the surface properties of cancer cells compared to normal cells. That is why ACPs are being investigated as potential candidates for cancer therapy. ACPs may be used alone or in combination with other treatment modalities like chemotherapy and radiation therapy. While ACPs hold promise as a novel approach to cancer treatment, there are challenges to overcome, including optimizing their stability, improving selectivity, and enhancing their delivery to cancer cells, continuous increasing in number of peptide sequences, developing a reliable and precise prediction model. In this work, we propose an efficient transformer-based framework to identify ACPs for by performing accurate a reliable and precise prediction model. For this purpose, four different transformer models, namely ESM, ProtBERT, BioBERT, and SciBERT are employed to detect ACPs from amino acid sequences. To demonstrate the contribution of the proposed framework, extensive experiments are carried on widely-used datasets in the literature, two versions of AntiCp2, cACP-DeepGram, ACP-740. Experiment results show the usage of proposed model enhances classification accuracy when compared to the literature studies. The proposed framework, ESM, exhibits 96.45% of accuracy for AntiCp2 dataset, 97.66% of accuracy for cACP-DeepGram dataset, and 88.51% of accuracy for ACP-740 dataset, thence determining new state-of-the-art. The code of proposed framework is publicly available at github (https://github.com/mstf-yalcin/acp-esm).

Cross-Species Applications of Peptide Substrate Reporters to Quantitative Measurements of Kinase Activity.

Peptide substrate reporters are short chains of amino acids designed to act as substrates for enzymes of interest. Combined with capillary electrophoresis and laser-induced fluorescence detection (CE-LIF), they are powerful molecular tools for quantitative measurements of enzyme activity even at the level of single cells. Although most peptide substrate reporters have been optimized for human or murine cells in health-related applications, their performance in nonmammalian organisms remains largely unexplored. In this study, we evaluated three peptide substrate reporters for protein kinase B (PKB) in two eukaryotic microbes, Dictyostelium discoideum and Tetrahymena thermophila, which are evolutionarily distant from mammals and from each other yet express PKB homologues. All three peptide substrate reporters were phosphorylated in lysates from both organisms but with varying phosphorylation kinetics and stability. To demonstrate reporter utility, we used one to screen for and identify the previously unknown stimulus needed to activate PHK5, the PKB homologue in T. thermophila. In D. discoideum, we employed the highly quantitative nature of these assays using CE-LIF to make precise measurements of PKB activity in response to transient stimulation, drug treatment, and genetic mutation. These results underscore the broad applicability of peptide substrate reporters across diverse species while highlighting the need for further research to determine effective peptide stabilization strategies across different biological contexts.

Corrigendum: Corrigendum to the Publication “A Modular Synthesis of Teraryl‐Based α‐Helix Mimetics, Part 5: A Complete Set of Pyridine Boronic Acid Pinacol Esters Featuring Side Chains of Proteinogenic Amino Acids”

Corrigendum: Corrigendum to the Publication “A Modular Synthesis of Teraryl‐Based α‐Helix Mimetics, Part 5: A Complete Set of Pyridine Boronic Acid Pinacol Esters Featuring Side Chains of Proteinogenic Amino Acids”

Keratin hydrolysate as a chrome exhaust aid and keratin filler in leather processing: A cleaner technology approach for tannery solid waste management and leather manufacturing

Hair burning unhairing and dampening of tannery wastes during the hair-saving unhairing process are becoming significant problems in the tanning industry. Therefore, this research article focuses on the extraction of keratin hydrolysate (KH) and its application as a chrome exhaust aid and keratin filler in leather manufacturing process. The structure, morphology and functional groups of the extract were examined using X-Ray Diffractometer (XRD), scanning electron microscopy (SEM) and Fourier transform infrared spectrometer (FTIR), respectively. To study and contrast the degree of improvement in chromium uptake, the KH solution was applied both before tanning on the pickled pelt and after tanning during basification. The thermal stability, physical strength characteristics and organoleptic properties of the leathers obtained were characterized. Furthermore, the environmental impact of the tanning system was assessed through a comparative analysis of the spent liquors. Finally, experimental retanning process was conducted to replace the commercial protein filler (Celatan F: 50, 75, and 100 %) with KH solution, with concurrent processing of control leather using conventional chrome tanning agent at 6 % dosage of chromium. The FTIR analysis of the extract confirmed the presence of alkyl side chains of amino acids as well as carboxylic, amide, carboxyl group and aldehyde functional groups at 1400-1700 cm−1,3,303.46 cm−1,3270 cm−1 and 2752 cm−1, respectively. XRD spectrum showed two diffraction peaks at 2 theta values of 9.36° and 21.16°, respectively. Leathers with improved mechanical strength, organoleptic properties and thermal stability were obtained with 100 % substitution of Celatan F at pH 6 and 10 % chromium dosage. It was also discovered that the shrinkage temperature of the experimental leather was enhanced to more than 105 °C. Environmental impact evaluation on the spent liquor showed that the complete replacement of Celatan F with KH solution brought about a notable decrease in COD and TDS in the spent liquor. The extraction and application of tannery hair waste-based keratin hydrolysate as an efficient, environmentally friendly chrome exhaust aid and keratin filler has been attempted and established in this research article.

Resolution of ribosomal stalling by EF-P and ABCF ATPases YfmR and YkpA/YbiT.

Efficiency of protein synthesis on the ribosome is strongly affected by the amino acid composition of the assembled amino acid chain. Challenging sequences include proline-rich motifs as well as highly positively and negatively charged amino acid stretches. Members of the F subfamily of ABC ATPases (ABCFs) have been long hypothesised to promote translation of such problematic motifs. In this study we have applied genetics and reporter-based assays to characterise the four housekeeping ABCF ATPases of Bacillus subtilis: YdiF, YfmM, YfmR/Uup and YkpA/YbiT. We show that YfmR cooperates with the translation factor EF-P that promotes translation of Pro-rich motifs. Simultaneous loss of both YfmR and EF-P results in a dramatic growth defect. Surprisingly, this growth defect can be largely suppressed though overexpression of an EF-P variant lacking the otherwise crucial 5-amino-pentanolylated residue K32. Using in vivo reporter assays, we show that overexpression of YfmR can alleviate ribosomal stalling on Asp-Pro motifs. Finally, we demonstrate that YkpA/YbiT promotes translation of positively and negatively charged motifs but is inactive in resolving ribosomal stalls on proline-rich stretches. Collectively, our results provide insights into the function of ABCF translation factors in modulating protein synthesis in B. subtilis.

Exploring the Use of a Lipopeptide in Dipalmitoylphosphatidylcholine Monolayers for Enhanced Detection of Glyphosate in Aqueous Environments.

The growing reliance on pesticides for pest management in agriculture highlights the need for new analytical methods to detect these substances in food and water. Our research introduces a SPRWG-(C18H37) lipopeptide (LP) as a functional analog of acetylcholinesterase (AChE) for glyphosate detection in environmental samples using phosphatidylcholine (PC) monolayers. This LP, containing hydrophilic amino acids linked to an 18-carbon aliphatic chain, alters lipid assembly properties, leading to a more flexible system. Changes included reduced molecular area and peak pressure in Langmuir adsorption isotherms. Small angle X-ray scattering (SAXS) and atomic force microscopy (AFM) analyses provided insights into the LP's structural organization within the membrane and its interaction with glyphosate (PNG). Structural and geometric parameters, as derived from in silico molecular dynamics simulations (MD), substantiated the impact of LP on the monolayer structure and the interaction with PNG. Notably, the presence of the LP and glyphosate increased charge transfer resistance, indicating strong adherence of the monolayer to the indium tin oxide (ITO) surface and effective pesticide interaction. A calibration curve for glyphosate concentration adjustment revealed a detection limit (LOD) of 24 nmol L-1, showcasing the high sensitivity of this electrochemical biosensor. This LOD is significantly lower than that of a similar colorimetric biosensor in aqueous media with a detection limit of approximately 0.3 μmol L-1. Such an improvement in sensitivity likely stems from adding a polar residue to the amino acid chain of the LP.

One-step high efficiency separation of prolyl endopeptidase from Aspergillus niger and its application

Prolyl endopeptidase from Aspergillus niger (An-PEP) is an enzyme that recognizes C-terminal peptide bonds of amino acid chains and cleaves them by hydrolysis. An aqueous two-phase system (ATPS) was used to separate An-PEP from fermentation broth. Through single factor experiments, the ATPS containing 16 % (w/w) PEG2000 and 15 % (w/w) (NH4)2SO4 at pH 6.0 obtained the recovery of 79.74 ± 0.16 % and the purification coefficient of 7.64 ± 0.08. It was then used to produce soy protein isolate peptide (SPIP) by hydrolysis of soy protein isolate (SPI), and SPIP-Ferrous chelate (SPIP-Fe) was prepared with SPIP and Fe2+. The chelation conditions were optimized by RSM, as the chelation time was 30 min, chelation temperature was 25 °C, SPIP mass to VC mass was two to one and pH was 6.0. The obtained chelation rate was 82.56 ± 2.30 %. The change in the structures and functional features of SPIP before and after chelation were investigated. The FTIR and UV–Vis results indicated that the chelation of Fe2+ and SPIP depended mainly on the formation of amide bonds. The fluorescence, SEM and amino acid composition analysis results indicated that Fe2+ could induce and stabilize the surface conformation and change the amino acid distribution on the surfaces of SPIP. The chelation of SPIP and Fe2+ resulted in the enhancement of radical scavenging activities and ACE inhibitory activities. This work provided a new perspective for the further development of peptide-Fe chelates for iron supplement.

Classification of bioactive peptides: A systematic benchmark of models and encodings

Bioactive peptides are short amino acid chains possessing biological activity and exerting physiological effects relevant to human health. Despite their therapeutic value, their identification remains a major problem, as it mainly relies on time-consuming in vitro tests. While bioinformatic tools for the identification of bioactive peptides are available, they are focused on specific functional classes and have not been systematically tested on realistic settings. To tackle this problem, bioactive peptide sequences and functions were here gathered from a variety of databases to generate a unified collection of bioactive peptides from microbial fermentation. This collection was organized into nine functional classes including some previously studied and some unexplored such as immunomodulatory, opioid and cardiovascular peptides. Upon assessing their sequence properties, four alternative encoding methods were tested in combination with a multitude of machine learning algorithms, from basic classifiers like logistic regression to advanced algorithms like BERT. Tests on a total of 171 models showed that, while some functions are intrinsically easier to detect, no single combination of classifiers and encoders worked universally well for all classes. For this reason, we unified all the best individual models for each class and generated CICERON (Classification of bIoaCtive pEptides fRom micrObial fermeNtation), a classification tool for the functional classification of peptides. State-of-the-art classifiers were found to underperform on our realistic benchmark dataset compared to the models included in CICERON. Altogether, our work provides a tool for real-world peptide classification and can serve as a benchmark for future model development.