Amino Acid Composition Of Peptides Research Articles

E-CLEAP: An ensemble learning model for efficient and accurate identification of antimicrobial peptides.

With the increasing problem of antimicrobial drug resistance, the search for new antimicrobial agents has become a crucial task in the field of medicine. Antimicrobial peptides, as a class of naturally occurring antimicrobial agents, possess broad-spectrum antimicrobial activity and lower risk of resistance development. However, traditional screening methods for antimicrobial peptides are inefficient, necessitating the development of an efficient screening model. In this study, we aimed to develop an ensemble learning model for the identification of antimicrobial peptides, named E-CLEAP, based on the Multilayer Perceptron Classifier (MLP Classifier). By considering multiple features, including amino acid composition (AAC) and pseudo amino acid composition (PseAAC) of antimicrobial peptides, we aimed to improve the accuracy and generalization ability of the identification process. To validate the superiority of our model, we employed five-fold cross-validation and compared it with other commonly used methods for antimicrobial peptide identification. In the experimental results on an independent test set, E-CLEAP achieved accuracies of 97.33% and 84% for the AAC and PseAAC features, respectively. The results demonstrated that our model outperformed other methods in all evaluation metrics. The findings of this study highlight the potential of the E-CLEAP model in enhancing the efficiency and accuracy of antimicrobial peptide screening, which holds significant implications for drug development, disease treatment, and biotechnology advancement. Future research can further optimize the model by incorporating additional features and information, as well as validating its reliability on larger datasets and in real-world environments. The source code and all datasets are publicly available at https://github.com/Wangsicheng52/E-CLEAP.

Characterization of Novel Cell-Adhesive Peptides for Biomaterial Development.

In previous studies, my group developed cell-adhesive peptide-polysaccharide complexes as biomaterials for tissue engineering. Having a wide variety of cell-adhesive peptides is important as the biological functions of peptide-polysaccharide complexes are highly dependent on the biological activity of peptides. This paper reviews the biological activities of two types of recently characterized cell-adhesive peptides. The first is peptides rich in basic amino acids originating from octaarginine. We analyzed the relationships between the amino acid composition of basic peptides and cell adhesion, elongation, and proliferation and identified the most suitable peptide for cell culture. The second was arginine-glycine-aspartic acid (RGD)-containing peptides that promote the adhesion of induced pluripotent stem cells (iPSCs). We identified the RGD-surrounding sequences necessary for iPSC adhesion, clarified the underlying mechanism, and improved cell adhesion by modifying the structure-activity relationships. The novel cell-adhesive peptides identified in our previous studies may aid in the development of novel peptide-based biomaterials.

Preparation, physicochemical properties, and formation mechanism of quinoa self-assembled peptide-based hydrogel

Currently, self-assembly peptides with hydrogel properties that are used in various applications are being chemically synthesized. These peptides not only have safety and environmental problems but are also expensive and cumbersome to prepare. The present study established a convenient and efficient method for producing plant-based peptides with decent gel-forming ability from quinoa proteins. After alkaline protease treatment, hydrogels made with quinoa protein hydrolysis exhibited potent self-assembly capacity, enhanced gel hardness, and improved rheological properties. Moreover, the microstructure results revealed that the quinoa peptide hydrogels had regular, uniform, and interconnected porous structures. These observations were primarily attributed to the hydrogen bonding force and hydrophobic aggregation caused by hydrophobic group exposure. Amino acid and proteomics analysis suggested that the amino acid composition and sequence of quinoa peptides significantly influenced the formation of self-assembled hydrogels. Overall, this study provided a cost-effective approach to improve the gelling ability of quinoa protein and could potentially replace the use of chemically synthesized peptides in various applications, laying the theoretical basis for the development of novel natural plant-based foods.

Identification of umami peptides from Wuding chicken by Nano-HPLC-MS/MS and insights into the umami taste mechanisms

Wuding chicken is popular with consumers in China because of its umami taste. This study aimed to identify novel umami peptides from Wuding chicken and explore the taste mechanism of umami peptides. The molecular masses and amino acid compositions of peptides in Wuding chicken were identified by nano-scale liquid chromatography-tandem mass spectrometry (Nano-HPLC-MS/MS). The taste characteristics of the peptides synthesized by the solid-phase method were evaluated by sensory evaluation combined with electronic tongue technology. The secondary structure of the peptides was further analyzed by circular dichroism (CD), and the relationship between the structure and taste of the peptides was elucidated by molecular docking. The results showed that eight potential umami peptides were identified, among which FVT (FT-3), LDF (LF-3), and DLAGRDLTDYLMKIL (DL-15) had distinct umami tastes, and FT-3 had the highest umami intensity, followed by LF-3 and DL-15. The relative contents of β-sheets in the three umami peptides were 55.20%, 57.30%, and 47.70%, respectively, which were the key components of Wuding chicken umami peptides. In addition to LF-3 embedded in the cavity-binding domain of the TIR1, both FT-3 and DL-15 were embedded in the venus flytrap domain (VFTD) of the T1R3 to bind the umami receptor T1R1/T1R3. The main binding forces between the umami peptides and the umami receptor T1R1/T1R3 relied on hydrogen bonds and hydrophobic interactions, and the key amino acid residues of the combination of umami peptides and the umami receptor T1R1/T1R3 were Glu292, Asn235, and Tyr262.

Comparison of deep learning models with simple method to assess the problem of antimicrobial peptides prediction.

Antibiotic-resistant strains are an emerging threat to public health. The usage of antimicrobial peptides (AMPs) is one of the promising approaches to solve this problem. For the development of new AMPs, it is necessary to have reliable prediction methods. Recently, deep learning approaches have been used to predict AMP. In this paper, we want to compare simple and complex methods for these purposes. We used the BERT transformer to create sequence embeddings and the multilayer perceptron (MLP) and light attention (LA) approaches for classification. One of them reached about 80 % accuracy and specificity in benchmark testing, which is on par with the best available methods. For comparison, we proposed a simple method using only the amino acid composition of proteins or peptides. This method has shown good results, at the level of the best methods. We have prepared a special server for predicting the ability of AMPs by amino acid composition: http://bioproteom.protres.ru/antimicrob/.

Application of steam explosion treatment on the collagen peptides extraction from cattle bone

In this study, steam explosion (SE) treatment was applied to extract collagen peptides from cattle bone. The SE treatment conditions included steam pressure: 1.5 MPa (200.43 °C), 2.0 MPa (213.85 °C), and 2.5 MPa (224.99 °C), and reaction time: 10 min, 20 min, and 30 min. With the increase of pressure and reaction time, the protein recovery rate improved, and reached to 60.5% at 2.0 MPa–30 min. SE significantly decreased the molecular weight of collagen peptides (P < 0.05) with increasing pressure and reaction time. However, at 2.5 MPa, SE darkened the sample color resulting in dark yellow. Particle size analysis and SEM images indicated that SE decreased the particle size and destroyed microstructure of cattle bone powder. FT-IR analysis showed that SE induced distinct characteristic peaks of hydroxyapatite in cattle bone powder. SE facilitated peptides release from collagen by destroying peptide bonds and enzymatic cross-links. Amino acid analysis indicated SE could not change the amino acid composition of collagen peptides. The calcium-binding ability and osteoblast proliferative activity of extracted collagen peptides were 44.7 μg/mg and 126.7% (200 μg/mL), respectively. The findings put forward data support and a scientific basis for the application and development of SE technology to collagen peptides extraction and high-value utilization of cattle bone.

Factors Influencing the Prediction Accuracy of Model Peptides in Reversed-Phase Liquid Chromatography

Hydrophobicity is an important physicochemical property of peptides in solution. As well as being strongly associated with peptide stability and aggregation, hydrophobicity governs the solution based chromatographic separation processes, specifically reversed-phase liquid chromatography (RPLC). In addition, hydrophobicity is a major physicochemical property of peptides in comparison to H-bonding, electrostatic, and aromatic properties in intermolecular interactions. However, a wide range of molecular factors can influence peptide hydrophobicity, with accurate predictions depending on specific peptide amino acid compositions, structure, and conformation. It is noticeable that peptide composition, the position of the amino acid, and its neighbouring groups play a crucial role in the elution process. In light of this, the same amino acid behaved differently depending on its position and neighbouring amino acid in the peptide chain. Extra attention should be paid to the denaturation process during the course of elution, as it has been shown to complicate and alter the elution pattern. This paper reports on the key peptide properties that can alter hydrophobicity and, consequently, the RPLC elution behaviour of the peptides, and it will conclude by proposing improved prediction algorithms for peptide elution in RPLC.

In vitro immunomodulatory and antioxidant effects of oligopeptides and four characteristic peptides in black-bone silky fowl (Gallus gallus domesticus Brisson).

Black-bone silky fowl (Gallus gallus domesticus Brisson) is considered to have strengthening effect on the body and immunomodulatory effects. The black-bone silky fowl peptide (BSFP) was produced by enzymatic digestion of the whole black-bone silky fowl (including the head and claws) after removal of the viscera. Afterwards, the four of the characteristic peptides Glu-Phe (EF), Glu-Glu-Leu (EEL), Glu-His-Pro-Thr (EHPT), Ala-Gly-Gly-His (AGGF) of the BSFP were identified by HPLC-MS/MS. The preventive effects of BSFP and the four characteristic peptides on antioxidant and immunomodulation were investigated. The antioxidant capacity was assessed by in vitro HepG2 intracellular reactive oxygen species (ROS). The immunomodulatory experiments were conducted by measuring the effects of the BSFP and four peptides on the proliferation of splenocytes, T and B lymphocytes cells, the CD4+ /CD8+ T lymphocytes ratio, and the phagocytic capacity of macrophages and the nitric oxide (NO) content of macrophages. The four peptides of BSFP showed strong antioxidant capacity, with the most potent peptide for intracellular ROS being AGGF, with 56% inhibition. AGGF, EF, and BSFP showed highly positive effects on splenocyte proliferation and when Concanavalin A (ConA) was used as a stimulus for T lymphocytes and lipopolysaccharide (LPS) as a stimulus for B lymphocytes, the peptides stimulated cell proliferation in a dose-dependent manner. Of these, EF, AGGF, and BSFP promoted the proliferation of T lymphocytes; EF, EHPT, and BSFP significantly promoted the proliferation of B lymphocytes. EHPT and BSFP increased the CD4+ /CD8+ ratio of T cells. Needle aspiration of neutral red was significantly promoted by macrophages treated with peptides other than EF. In addition, EEL, EHPT, AGGF, and BSFP had a promotive effect on NO production in phagocytes. The results indicate that BSFP is a peptide product with good immunomodulatory functions, four peptides identified from BSFP show outstanding effects in terms of antioxidant properties and immunomodulation. PRACTICAL APPLICATIONS: In this study, the amino acid composition and relative molecular masses of the black-bone silky fowl peptide were analyzed, while the four peptides with significant effects on antioxidant and immunomodulatory properties in black-bone silky fowl peptide were identified by HPLC-MS/MS technique. Positive effects of black-bone silky fowl peptide and its four peptides on antioxidant capacity and immunomodulatory ability as revealed by cell experiments. The results of this experiment provide a preliminary theoretical basis for the development of new functional foods using black-bone silky fowl peptide and their characteristic peptides.

Characterization of peptides available to different bifidobacteria

Nitrogen source is a limiting factor for bifidobacterial growth. It is generally believed that the nitrogen metabolism system varies a lot in bifidobacteria, which has a low utilization efficiency of nitrogen sources in the medium. This study aimed to analyze the rules of peptide utilization and to improve the utilization efficiency of nitrogen sources in bifidobacteria. Casein hydrolysates were prepared to assess their growth-promoting effects on different Bifidobacterium. The quantity, molecular weight, and amino acid composition of transportable peptides in each strain were analyzed by ultrafiltration, gel chromatography, and nano-LC-MS/MS. The results revealed that bifidobacteria had a high affinity for hydrophilic peptides containing growth-promoting amino acids and the transportable peptides varied among the strains. B. bifidum could transport peptides containing up to 14 residues and had a high preference for peptides containing 2, 3, or 9 residues. While B. longum could transport peptides containing up to 20 residues and B. brevis mainly transported peptides with 2–4 and 8–20 residues. Significant differences in the amino acid and peptide transport systems were revealed by the genome sequence analysis. This study highlighted the importance of specific peptides as nitrogen sources rather than macromolecules, which can significantly promote the growth of different bifidobacteria.

An immunological glimpse of human virus peptides: Distance from self, MHC class I binding, proteasome cleveage, TAP transport and sequence composition entropy

Adaptive immune response is triggered when specific pathogen peptides called epitopes are recognised as exogenous according to the paradigm of self/non-self. To be recognized by immune cells, epitopes have to be exposed (presented) on the surface of the cell. Predicting if a peptide is exposed is important to shed light on the rules that govern immune response and, thus, identify potential targets and design vaccine and drugs. We focused on peptides exposed on cell surface and made accessible to immune system through the MHC Class I complex. Before this can happen, three successive selection steps have to take place: a) Proteasome cleveage, b) TAP Transport, and c) binding to MHC-class I. Starting from a set of 211 host human reference viruses, we computed the set of unique peptides occurring in the correspondent proteomes. Then, we obtained the probability values of Proteasome Cleveage, TAP Transport and Binding to MHC Class I associated to those peptides through established prediction software tools. Such values were analysed in conjunction with two other features that could play a major role: the distance from self, strictly linked to the concept of nullomers, and the sequence entropy, measuring the complexity of the peptide amino acid composition. The analysis confirmed and extended previous results on a larger, more significant and consistent data set; we showed that the higher the distances from self, the higher the score of TAP Transport and binding to MHC class I; no significant association was instead found between distance from self and Proteasome Cleveage. Additionally, amino acid peptide composition entropy was significantly associated with the other features. In particular, higher entropies were linked with higher scores of Proteasome Cleveage, TAP Transport, Binding to MHC Class I, and higher distance from self. The relationship among the three selection steps provided evidence of a tight inter-correlation, clearly suggesting it could be the product of a co-evolutive process. We believe that these results give new insights on the complex processes that regulate peptide presentation through MHC class I, and unveil the mechanisms the allow the immune system to distinguish self and viral non-self peptides.

Covalent Capture of a Collagen Mimetic Peptide with an Integrin-Binding Motif.

Collagen mimetic peptides (CMPs) are an excellent model to study the structural and biological properties of the extracellular matrix (ECM) due to ease of synthesis and variability in sequence. To ensure that synthetic materials accurately mimic the structure and function of natural collagen in the ECM, it is necessary to conserve the triple helix. However, CMP folding is subject to equilibrium, and frequently peptides exist in solution as both monomer and triple helix. Additionally, the stability of CMPs is highly dependent on peptide length and amino acid composition, leading to suboptimal performance. Here, we report the utility of covalent capture, a method to (a) direct the folding of a supramolecular triple helix and (b) form isopeptide bonds between the helix strands, in the design of an integrin-binding peptide with a GFOGER motif. Covalent capture effectively locked the triple helix and yielded a peptide with high thermal stability and a rapid folding rate. Compared to supramolecular triple helices bearing the same GFOGER-binding site, cell adhesion was substantially increased. In vitro assays using EDTA/Mg2+ and an anti-α2β1 antibody demonstrated the preservation of the high specificity of the binding event. This covalently captured integrin-binding peptide provides a template for the future design of bioactive ECM mimics, which can overcome limitations of supramolecular approaches for potential drug and biomaterial designs.

Resemblance-Ranking Peptide Library to Screen for Binders to Antibodies on a Peptidomic Scale.

A novel resemblance-ranking peptide library with 160,000 10-meric peptides was designed to search for selective binders to antibodies. The resemblance-ranking principle enabled the selection of sequences that are most similar to the human peptidome. The library was synthesized with ultra-high-density peptide arrays. As proof of principle, screens for selective binders were performed for the therapeutic anti-CD20 antibody rituximab. Several features in the amino acid composition of antibody-binding peptides were identified. The selective affinity of rituximab increased with an increase in the number of hydrophobic amino acids in a peptide, mainly tryptophan and phenylalanine, while a total charge of the peptide remained relatively small. Peptides with a higher affinity exhibited a lower sum helix propensity. For the 30 strongest peptide binders, a substitutional analysis was performed to determine dissociation constants and the invariant amino acids for binding to rituximab. The strongest selective peptides had a dissociation constant in the hundreds of the nano-molar range. The substitutional analysis revealed a specific hydrophobic epitope for rituximab. To show that conformational binders can, in principle, be detected in array format, cyclic peptide substitutions that are similar to the target of rituximab were investigated. Since the specific binders selected via the resemblance-ranking peptide library were based on the hydrophobic interactions that are widespread in the world of biomolecules, the library can be used to screen for potential linear epitopes that may provide information about the cross-reactivity of antibodies.

Structural Basis for the Peptidoglycan-Editing Activity of YfiH.

ABSTRACTBacterial cells are encased in peptidoglycan (PG), a polymer of disaccharide N-acetylglucosamine (GlcNAc) and N-acetyl-muramic acid (MurNAc) cross-linked by peptide stems. PG is synthesized in the cytoplasm as UDP-MurNAc-peptide precursors, of which the amino acid composition of the peptide is unique, with l-Ala added at the first position in most bacteria but with l-Ser or Gly in some bacteria. YfiH is a PG-editing factor whose absence causes misincorporation of l-Ser instead of l-Ala into peptide stems, but its mechanistic function is unknown. Here, we report the crystal structures of substrate-bound and product-bound YfiH, showing that YfiH is a cytoplasmic amidase that controls the incorporation of the correct amino acid to the nucleotide precursors by preferentially cleaving the nucleotide precursor by-product UDP–MurNAc–l-Ser. This work reveals an editing mechanism in the cytoplasmic steps of peptidoglycan biosynthesis.

Construction of a water‐in‐oil‐in‐water (W/O/W) double emulsion system based on oyster peptides and characterisation of freeze‐dried products

AbstractIn order to broaden the range of applications for oyster peptides in the food field, the amino acid composition of oyster peptide was analysed, after which the peptide sequence was identified using liquid‐mass spectrometry technology. A W1/O/W2 double emulsion was prepared by the two‐step shear emulsification method. The W1/O/W2 double emulsion was further freeze‐dried after addition of alginate to obtain the final product, and the characteristics of the related product were analysed. The results show that oyster peptides are mainly composed of short peptides with molecular weights between 459.3 Da and 2716.3 Da. Polyglycerol polyrinoleate (PGPR) was selected as the emulsifier and added at 5% of the mass of the oil phase. The mass ratio of the oil phase to the water phase was O:W = 6:4, and optimal stability of the W1/O emulsion was obtained by shearing and emulsifying for 2 min at 12 000 rpm. A superior W1/O/W2 double emulsion can be obtained by secondary emulsification in which the hydrophilic emulsifier Tween 80 was added at 0.8% (w/w) of the mass of the external water phase (W2). The mass ratio of the emulsion to the external water phase was 5:5. The lyophilised product has good re‐solubility, with the reconstituted emulsion maintaining the double‐emulsion structure. Electronic nose results showed that the peculiar smell of the reconstituted emulsion was significantly lower than that of the oyster peptide solution. The results of this research provide a reference for the development and application of oyster peptides in the field of functional health foods.

Rapid enantioselective amino acid analysis by ultra-high performance liquid chromatography-mass spectrometry combining 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate derivatization with core-shell quinine carbamate anion exchanger separation

Amino acid analysis (AAA) is of central importance for the characterization of the amino acid composition of proteins, peptides, pharmaceutical formulations, dietary supplements, in bioanalysis and metabolomics. Common methodologies are based on achiral assays and hence do not consider distinction of D and L-amino acid enantiomers. This may be misleading in many instances, because therapeutic peptides and natural peptides synthesized by non-ribosomal peptide synthetases (NRPSs) frequently contain D-amino acids to achieve proteolytic stability. Furthermore, stereochemical integrity control of peptides made from L-amino acids also need stereoselective assays, and racemization in natural products (proteins, peptides, amino acids) have shown to be useful biomarkers of disease and require assays, which can provide information about the individual stereoisomers. Hence, rapid enantioselective amino acid analysis (ReAAA) is of utmost importance. However, currently employed enantioselective assays are often only focusing on a limited number of amino acids or require long analysis times making them incompatible for high-throughput sample analysis. Here, we present an ReAAA assay, which is based on a fast UHPLC enantiomer separation using a short QN-AX core-shell particle column (2.7 µm) coupled to electrospray ionization quadrupole time of flight mass spectrometric (ESI-QTOF-MS) detection. Amino acid samples are mixed with a [u-13C15N]-labelled L- or DL-amino acid standard mixture, precolumn derivatized with 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate (AQC) reagent and subjected to UHPLC-ESI-MS analysis. A number of chromatographic variables have been optimized (buffer additives and concentration, water content, flow rate and temperature) to achieve the goal of simultaneous amino acid enantiomer separation of all proteinogenic amino acids within the shortest possible analysis time. A mobile phase consisting of 50 mM NH4FA, 50 mM FA and 0.5% H2O in MeOH combined with a flow rate of 1 mL/min and a column temperature of 30 °C has been identified as optimal. With these conditions, all of the proteinogenic DL-enantiomers (except for Arg) can be separated in less than 2.5 min. If D-Arg and distinction between D-Leu/D-Ile is of concern, a second-tier method can accomplish this goal. The method can be very useful for ReAAA when high sample throughput is a major demand. Its utility was demonstrated by ReAAA of a lipopeptide hydrolysate which contained several D-amino acids and of an amino acid supplement in which minor D-amino acid impurities could be detected.

WRAP-based nanoparticles for siRNA delivery: a SAR study and a comparison with lipid-based transfection reagents

Recently, we designed novel amphipathic cell-penetrating peptides, called WRAP, able to transfer efficiently siRNA molecules into cells. In order to gain more information about the relationship between amino acid composition, nanoparticle formation and cellular internalization of these peptides composed of only three amino acids (leucine, arginine and tryptophan), we performed a structure–activity relationship (SAR) study. First, we compared our WRAP1 and WRAP5 peptides with the C6M1 peptide also composed of the same three amino acids and showing similar behaviors in siRNA transfection. Afterwards, to further define the main determinants in the WRAP activity, we synthesized 13 new WRAP analogues harboring different modifications like the number and location of leucine and arginine residues, the relative location of tryptophan residues, as well as the role of the α-helix formation upon proline insertions within the native WRAP sequence. After having compared the ability of these peptides to form peptide-based nanoparticles (PBNs) using different biophysical methods and to induce a targeted gene silencing in cells, we established the main sequential requirements of the amino acid composition of the WRAP peptide. In addition, upon measuring the WRAP-based siRNA transfection ability into cells compared to several non-peptide transfection agents available on the markets, we confirmed that WRAP peptides induced an equivalent level of targeted gene silencing but in most of the cases with lower cell toxicity as clearly shown in clonogenic assays.

Effects of poultry raw material variation and choice of protease on protein hydrolysate quality

The aim of this study was to investigate the role of compositional variations in side-streams from the chicken and turkey industry on product characteristics after enzymatic protein hydrolysis (EPH). Variation was obtained using four raw materials, namely chicken and turkey carcasses, and mechanically deboned chicken and turkey residues. Alcalase 2.4 L, Corolase 2TS and Flavourzyme, three commercial proteases with different specificities, were used to investigate impact of protease choice on product characteristics. Besides protein yield, effects on product characteristics such as nutrient and amino acid composition, size distribution of peptides, degree of hydrolysis (DH%), rheological properties, and angiotensin-I-converting enzyme (ACE) inhibition, were investigated. Results show that choice of protease and industrially relevant variations in poultry raw material composition both have major effect on product composition and the other quality parameters studied. Protein yield, proximate composition, and bioactivity were more affected by protease than raw material variation. Raw material variation had a bigger impact on quality parameters such as peptide size distribution and amino acid composition, exemplified by the sum of essential amino acids. This means that raw material variation should be handled and accounted for to realize the true potential that exists in tailor-making EPH products with specified properties for targeted applications.

Enzymolysis peptides from Mauremys mutica plastron improve the disorder of neurotransmitter system and facilitate sleep-promoting in the PCPA-induced insomnia mice

Ethnopharmacology relevancyFor many centuries, Mauremys mutica is highly valued as a food homologous Chinese herbal medicine. It has been considered useful to sedate, nourish brain and promote sleep. However, the animal experimental evidence of its sleep-promoting activity is missing in literature. Aim of the studyIn this study, PCPA-induced insomnia model was used to explore the sleep-promoting mechanism of enzymolysis peptides from PMM, and its main composition and chemical structure were analyzed. Materials and methodsExperiments were performed using PCPA-induced insomnia model, all animals were intraperitoneally injected with PCPA (350 mg/kg·d) for two days. The sleep-promoting effect evaluated using measuring content of 5-HT, GABA, DA, IL-1, BDNF and expression of 5-HT1A receptor and GABAA receptor α1-subunit in mice brain. Primary structure of peptides was identified by HPLC-ESI-QqTOF-MS/MS. ResultsCompared with the model group, the content of 5-HT, GABA, IL-1, BDNF in mice brain of PMM peptide groups was increased to varying degrees, the content of DA was decreased, and the gene transcription and protein expression of 5-HT1A receptor and GABAA receptor α1-subunit were almost all returned to normal levels. In addition, the primary structures of most abundant nine typical peptides in PMM peptides were identified. ConclusionsThe results showed that PMM peptides could improve the disorder of neurotransmitter system, restore compensatory over-expression 5-HT1A receptor and GABAA receptor α1-subunit, and have a good sleep-promoting effect. The specific amino acid composition, sequence and glycosylation modification of PMM peptides may be the key reason for their activity, which lays a foundation for the subsequent development of sleep-promoting peptide products.

The Choice of Search Engine Affects Sequencing Depth and HLA Class I Allele-Specific Peptide Repertoires

Standardization of immunopeptidomics experiments across laboratories is a pressing issue within the field, and currently a variety of different methods for sample preparation and data analysis tools are applied. Here, we compared different software packages to interrogate immunopeptidomics datasets and found that Peaks reproducibly reports substantially more peptide sequences (~30–70%) compared with Maxquant, Comet, and MS-GF+ at a global false discovery rate (FDR) of <1%. We noted that these differences are driven by search space and spectral ranking. Furthermore, we observed differences in the proportion of peptides binding the human leukocyte antigen (HLA) alleles present in the samples, indicating that sequence-related differences affected the performance of each tested engine. Utilizing data from single HLA allele expressing cell lines, we observed significant differences in amino acid frequency among the peptides reported, with a broadly higher representation of hydrophobic amino acids L, I, P, and V reported by Peaks. We validated these results using data generated with a synthetic library of 2000 HLA-associated peptides from four common HLA alleles with distinct anchor residues. Our investigation highlights that search engines create a bias in peptide sequence depth and peptide amino acid composition, and resulting data should be interpreted with caution.

Crocodylus porosus: a potential source of anticancer molecules

BackgroundCancer remains a global threat resulting in significant morbidity and mortality despite advances in therapeutic interventions, suggesting urgency for identification of anticancer agents. Crocodiles thrive in polluted habitat, feed on...