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Human leukocyte antigen (HLA) recognizes foreign threats and triggers immune responses by presenting peptides to T cells. Computationally modeling the binding patterns between peptide and HLA is very important for the development of tumor vaccines. However, it is still a big challenge to accurately predict HLA molecules binding peptides. In this paper, we develop a new model TripHLApan for predicting HLA molecules binding peptides by integrating triple coding matrix, BiGRU + Attention models, and transfer learning strategy. We have found the main interaction site regions between HLA molecules and peptides, as well as the correlation between HLA encoding and binding motifs. Based on the discovery, we make the preprocessing and coding closer to the natural biological process. Besides, due to the input being based on multiple types of features and the attention module focused on the BiGRU hidden layer, TripHLApan has learned more sequence level binding information. The application of transfer learning strategies ensures the accuracy of prediction results under special lengths (peptides in length 8) and model scalability with the data explosion. Compared with the current optimal models, TripHLApan exhibits strong predictive performance in various prediction environments with different positive and negative sample ratios. In addition, we validate the superiority and scalability of TripHLApan's predictive performance using additional latest data sets, ablation experiments and binding reconstitution ability in the samples of a melanoma patient. The results show that TripHLApan is a powerful tool for predicting the binding of HLA-I and HLA-II molecular peptides for the synthesis of tumor vaccines. TripHLApan is publicly available at https://github.com/CSUBioGroup/TripHLApan.git. [ABSTRACT FROM AUTHOR]

Required metrological tools, such as higher order reference measurements procedures, pure substance and matrix certified reference materials, are established for small well defined molecules. Difficulties still remain in the provision of SI traceable standards in the area of larger biomolecules such as peptides/proteins. The provision of Primary Calibration Reference Services has been identified as a core technical competency for National Measurement Institutes (NMIs). A concept has been elaborated by the Focus Group I on peptide/protein purity for the strategic planning of ongoing Key Comparisons of the Protein Analysis Working Group (PAWG) within the Comité Consultatif pour la Quantité de Matière (CCQM). The assignment of the mass fraction content of high purity peptide/protein materials will be the subject of the CCQM-K115/P55.2 comparison series to directly support NMI services and certified reference materials currently being provided by NMIs. [ABSTRACT FROM AUTHOR]

A simple method is described for the patterned deposition of Teflon on paper to create an integrated platform for parallel organic synthesis and cell-based assays. Solvent-repelling barriers made of Teflon-impregnated paper confine organic solvents to specific zones of the patterned array and allow for 96 parallel flow-through syntheses on paper. The confinement and flow-through mixing significantly improves the peptide yield and simplifies the automation of this synthesis. The synthesis of 100 peptides ranging from 7 to 14 amino acids in length gave over 60 % purity for the majority of the peptides (>95 % yield per coupling/deprotection cycle). The resulting peptide arrays were used in cell-based screening to identify 14 potent bioactive peptides that support the adhesion or proliferation of breast cancer cells in a 3D environment. In the future, this technology could be used for the screening of more complex phenotypic responses, such as cell migration or differentiation. [ABSTRACT FROM AUTHOR]

There has been growing discovery and use of therapeutic peptides in drug delivery and tissue engineering. Peptides are smaller than proteins and can be formulated into drug delivery systems without significant loss of their bioactivity, which remains a concern with proteins. However, the smaller size of peptides has made the controlled release of these bioactive molecules from carriers challenging. Thus, there has been increasing development of carriers to improve the controlled release of peptides by leveraging hydrophobic and electrostatic interactions between the peptide and the carrier. The focus of this review paper is to critically discuss synthetic and natural nanoparticles and microparticles that have been investigated for the controlled delivery of peptides with emphasis on the underlying interactions. [Display omitted] [ABSTRACT FROM AUTHOR]

Proteins are the carriers of biological structure and function, which are involved in almost all the physiological processes in organisms. The qualitative and quantitative analysis of proteins can not only help us understand the mechanisms of life activities, but also screen for the proteins with abnormal expression compared to healthy controls as biomarkers of diseases as well as environmental exposure to harmful substances, thus facilitating to unravel the mechanisms of disease generation and development. Tandem mass spectrometry (MS/MS) is currently the main tool for high-throughput proteomics analysis. It can characterize the proteins by determining the molecular mass of digestion products, locating modification sites, and obtaining sequence information. However, acidic amino acid residues often have a significant impact on the cleavage process of peptides, limiting the performance of MS/MS. For example, for the phosphopeptides containing abundance of negatively charged carboxyl and phosphoryl groups, their ionization is not efficient in the positive mode, and neutral loss is easy to occur during the cleavage process, resulting in a low coverage of product ions in the MS/MS spectra. In this paper, the carboxyl groups from the R group of aspartic acid and glutamic acid as well as the C-terminus of peptide were neutralized using dimethylamine derivatization under mild condition. Accordingly, the fragmentation features of peptides with altered charge properties were studied in collision-induced dissociation (CID) mode. Further, the peptides were labeled using light and heavy isotopic dimethylamine, respectively, thus enabling to verify the features based on the same ion with different labels. The results showed that the precursor ion signal from the derivatized peptide was significantly enhanced compared to that of the native peptide. And, the derived peptides could yield a variety of a, b, y, and z ions, and some reported ions in MS/MS analysis, such as the ion at m/z 129.10/135.14 produced by the peptides with glutamic acid or lysine residue at C-terminus, which facilitating to determine the C-terminal amino acid of protein. While, the peptides proned to lose the derivative groups located at the C-terminus, yielding a series of ions at m/z ［yn-45.06］ or ［yn-73.05] In addition, the neutralization of carboxyl groups could suppress the loss of phosphoryl groups in phosphopeptides to a certain extent, thus improving the resolution efficiency of the MS/MS spectra. Overall, the derivatization method based on carboxyamidation can provide abundant information for the sequence determination and quantitative analysis of peptides due to the altered fragmentation features in CID mode. [ABSTRACT FROM AUTHOR]

Temporins are short peptides secreted by frogs from all over the world. They exert antimicrobial activity, mainly against Gram-positive bacteria, including resistant pathogens; recent studies highlight other possible applications of these peptides as anticancer or antiviral agents. This review is meant to describe the main features of temporins produced by different ranid genera. Due to the abundance of published papers, we focus on the most widely investigated peptides. We report studies on their mechanism of action and three-dimensional structure in model systems mimicking bacterial membranes or in the presence of cells. The design and the antimicrobial activity of peptide analogues is also described, with the aim of highlighting elements that are crucial to improve the bioactivity of peptides while reducing their toxicity. Finally, a short section is dedicated to the studies aimed at applying these peptides as drugs, to produce new antimicrobial materials or in other technological uses. [ABSTRACT FROM AUTHOR]

Obtaining compounds with specificity for certain isoforms of ion channels is a significant problem of curent physiology and pharmacology. In a series of papers, we have shown that the α-hairpinin fold can serve as a template for the rational design of peptide ligands of potassium channels. Here, we used molecular modeling to optimize the structure of the previously obtained Tk-hefu-10 peptide, a selective KV1.3 channel blocker, with a half-maximal inhibitory concentration (IC50) of ≈150 nM. Molecular dynamics simulation of the Tk-hefu-10–KV1.3 complex provided information on the interaction of individual amino acid residues of the peptide and channel, and the analysis of these interactions made it possible to propose amino acid substitutions in the structure of Tk-hefu-10 to increase its affinity. Novel Tk-hefu-12 peptide is a truncated analog of Tk-hefu-10 by one residue with five substitutions; it is characterized by an IC50 value of ≈70 nM against KV1.3. In addition, there are no methionine residues in the structure of Tk-hefu-12, which makes it possible to obtain Tk-hefu peptides using cyanogen bromide. [ABSTRACT FROM AUTHOR]

Studies on peptide-based emulsifiers in the field of foods have progressed rapidly in the last decade, due to the higher anti-oxidative activity, faster adsorption to the interfaces, reduced allergenicity and higher nutritional values, compared to proteins used as emulsifiers. Peptides therefore have the potential for broader applications in emulsion-based foods. This paper provides an update on the current knowledge of the surface behavior of surface-active peptides and peptide assemblies. Factors affecting physical and oxidative stability of peptide-stabilized emulsions and the fabrication and utilization of peptide-associated conjugates in emulsions have also been summarized. The potential applications of peptide-stabilized emulsions in the food industry are finally discussed. Peptides with different primary and secondary structures show different surface behavior. Surface-active peptides with facial amphiphilicity can orient horizontally at the interfaces, while those with half hydrophobic-half hydrophilic residues orient perpendicularly at the interfaces. In addition, peptide assemblies with supermolecular structures can embed in the oil-water interfaces. The long-chain peptides with molecular weights of higher than 5 kDa usually exhibit better emulsifying capacity than short-chain peptides, and many factors (e.g., pH, temperature and ionic strength) can influence the physical stability of peptide-stabilized emulsions. Moreover, the presence of peptides can improve the oxidative stability of emulsions by repulsing or chelating metals. The fabrication of peptides into conjugates with polysaccharides, flavonoids, or phenols can further improve their emulsifying capacity. Finally, peptide-stabilized emulsions have been reported to be used as encapsulation materials or stabilizers/antioxidants in real emulsion-based food systems. • Protein hydrolysis is the mostly used method to prepare emulsifying peptide. • Primary and secondary structures of peptide affect their orientation at interfaces. • Environmental conditions influence the physical and oxidative stability of peptide-stabilized emulsions. • The stability of peptide-stabilized emulsions can be improved by using peptide conjugates. • Peptide-based emulsions can be used in delivery systems and real food systems. [ABSTRACT FROM AUTHOR]

Peptides have been used as components in biological analysis and fabrication of novel sensors due to several reasons, including well-known synthesis protocols, diverse structures, and acting as highly selective substrates for enzymes. Bio-conjugation strategies can provide a simple and efficient way to convert peptide-analyte interaction information into a measurable signal, which can be further used for the manufacture of new peptide-based biosensors. This paper describes the sensitive properties of a peptide-modified graphene oxide screen-printed carbon electrode for accurate and sensitive detection of a natural polyphenol antioxidant compound, namely rosmarinic acid. Glutaraldehyde was chosen as the cross-linking agent because it is able to bind nonspecifically to the peptide. We demonstrated that the strong interaction between the immobilized peptide on the surface of the sensor and rosmarinic acid favors the addition of rosmarinic acid on the surface of the electrode, leading to an efficient preconcentration that determines a high sensitivity of the sensor for the detection of rosmarinic acid. The experimental conditions were optimized using different pH values and different amounts of peptide to modify the sensor surface, so that its analytical performances were optimal for rosmarinic acid detection. By using cyclic voltammetry (CV) as a detection method, a very low detection limit (0.0966 μM) and a vast linearity domain, ranging from 0.1 µM to 3.20 µM, were obtained. The novelty of this work is the development of a novel peptide-based sensor with improved performance characteristics for the quantification of rosmarinic acid in cosmetic products of complex composition. The FTIR method was used to validate the voltammetric method results. [ABSTRACT FROM AUTHOR]

Peptides, short stretches of amino acids or small proteins that occupy a strategic position between proteins and amino acids, are readily accessible by chemical and biological methods. With ideal properties for forming high-affinity and specific interactions with host target proteins, they have established an important niche in the drug development spectrum complementing small molecule and biological therapeutics. Among the most successful biomedicines in use today, peptide-based drugs show great promise. This, coupled with recent advances in synthetic and nanochemical biology, has led to the creation of tailor-made peptide therapeutics for improved biocompatibility. This review presents an overview of the latest research on pathogen-derived, host-cell-interacting peptides. It also highlights strategies for using peptide-based therapeutics that address cellular transport challenges through the introduction of nanoparticles that serve as platforms to facilitate the delivery of peptide biologics and therapeutics for treating various inflammatory diseases. Finally, this paper describes future perspectives, specific pathogen-based peptides that can enhance specificity, efficiency, and capacity in functional peptide-based therapeutics, which are in the spotlight as new treatment alternatives for various diseases, and also presents verified sequences and targets that can increase chemical and pharmacological value. [Display omitted] • Pathogen-derived peptides attractive for the development of novel therapeutic. • Functional peptide-based therapeutics as new treatment for various diseases. • Peptide-based drug development verified can increase chemical and pharmacological value. [ABSTRACT FROM AUTHOR]

(1) Background: Disfunctions in autophagy machinery have been identified in various conditions, including neurodegenerative diseases, cancer, and inflammation. Among mammalian autophagy proteins, the Atg8 family member GABARAP has been shown to be greatly involved in the autophagy process of prostate cancer cells, supporting the idea that GABARAP inhibitors could be valuable tools to fight the progression of tumors. (2) Methods: In this paper, starting from the X-ray crystal structure of GABARAP in a complex with an AnkirinB-LIR domain, we identify two new peptides by applying in silico drug design techniques. The two ligands are synthesized, biophysically assayed, and biologically evaluated to ascertain their potential anticancer profile. (3) Results: Two cyclic peptides (WC8 and WC10) displayed promising biological activity, high conformational stability (due to the presence of disulfide bridges), and Kd values in the low micromolar range. The anticancer assays, performed on PC-3 cells, proved that both peptides exhibit antiproliferative effects comparable to those of peptide K1, a known GABARAP inhibitor. (4) Conclusions: WC8 and WC10 can be considered new GABARAP inhibitors to be employed as pharmacological tools or even templates for the rational design of new small molecules. [ABSTRACT FROM AUTHOR]

Neoantigen is a protein produced by mutant gene, which is only expressed in tumor cells. It is an ideal target for therapeutic tumor vaccines. Although synthetic long peptide (SLP)-based neoantigen vaccine, DNA-based neoantigen vaccine, and mRNA-based neoantigen vaccine are all in the development stage, they have some inherent shortcomings. Therefore, researchers turned their attention to a new type of "non-coding RNA (ncRNA)", circular RNA (circRNA), for potential better choice. Because of its unique high stability and protein-coding capacity, circRNA is a promising target in the field of neoantigen vaccine. In this paper, we reviewed the feasibility of circRNA encoding neoantigens, summarized the construction process, explained the mechanism of circRNA vaccine in vitro , and discussed the advantages and disadvantages of circRNA vaccine and possible combination with other immunotherapies. • Tumor vaccine is a new direction of cancer prevention and treatment. • Tumor neoantigens are tumor specific proteins and are ideal targets for tumor vaccines. • circRNA can be used as a vector for tumor vaccines because of its ability to encode small peptides. • In this paper, the construction method and application prospect of circRNA vaccine are described in detail. [ABSTRACT FROM AUTHOR]

Peptides exhibit various functional properties and bioactivities, and have been widely investigated and used in food area. However, using peptides alone may show some drawbacks, such as the undesirable stability of peptide-stabilized emulsions during storage, and the diminished bioactivities and the occurrence of peptide-induced celiac disease during digestion. The addition of polyphenols may help to solve above issues by the formation of peptide-polyphenol complexes. This paper provides a comprehensive review of covalent and non-covalent interactions between peptides and polyphenols. The influence of such interactions in bioactivity, antimicrobial property, sensitivity (i.e., causing celiac disease), and emulsifying property of peptides is also discussed. Hydrophobic interactions, hydrogen bonds, electrostatic interaction, and van der Waals interactions are the main non-covalent bondings involving in the formation of peptide-polyphenol complexes. The properties of peptides and polyphenols, the ratio of peptide/polyphenol, and the environmental conditions are the main factors influencing such non-covalent interactions. Oxidized peptides or reactive peptide radicals can also interact with polyphenols trough covalent interactions, and the properties of peptides and polyphenols can influence these interactions. In addition, the presence of polyphenols in peptide-polyphenol complexes can show synergetic or subtractive effect on bioactive peptides through various mechanisms. In contrary, the inhibiting effect of polyphenols on the digestion, absorption and recognition of peptides can help to improve the safety of celiac disease-related peptides. Moreover, the formation of peptide-polyphenol complexes can also improve the physical and oxidative stability of peptide-stabilized emulsions. • The impact of forming peptide-polyphenol complexes on the properties of peptides is reviewed. • The peptide-polyphenol complexes can be obtained by covalent or non-covalent bonds. • The presence of polyphenols enhances or diminishes the bioactivities of peptides. • The presence of polyphenols improves the safety of celiac disease-related peptides. • The formation of complexes can also improve the emulsifying properties of peptides. [ABSTRACT FROM AUTHOR]

• Two-dimensional separations enable peak purity analysis of pharmaceutical peptides. • Strategy to derive second-dimension gradient conditions. • Preferred gradient conditions discovered by retention modelling. The importance of therapeutic peptides continues to increase in the marketplace for treating a range of diseases including diabetes and obesity. Quality control analyses for these pharmaceutical ingredients usually depends on reversed-phase liquid chromatography, and it is critically important to ensure that no impurities coelute with the target peptide at levels that would compromise the safety or effectiveness of the drug products. This can be challenging due to the broad range of properties of impurities that can be present on one hand (e.g., amino acid substitutions, chain cleavages, etc.), and the similarity of other impurities on the other hand (e.g., d -/ l -isomers). Two-dimensional liquid chromatography (2D-LC) is a powerful analytical tool that is well suited to address this particular problem; the first dimension can be used to detect impurities over a broad range in properties, while the second dimension can be used to focus specifically on those species that might coelute with the target peptide in the first dimension. While hundreds of papers have been published on the use of 2D-LC for proteomics applications, there are very few papers that have focused on its use for characterisation of therapeutic peptides. This paper is the second in a two-part series. In Part I of the series, we studied several different column / mobile phase combinations that could be useful in 2D-LC separations of therapeutic peptides, with a focus on selectivity, peak shape, and complementarity to other combinations, particularly for isomeric peptides under mass spectrometry-friendly conditions (i.e., volatile buffers). In this second part in the series, we describe a strategy to derive second-dimension (2D) gradient conditions that both, ensure elution from the 2D column, and increase the likelihood of resolving peptides with very similar properties. We find that a two-step process yields conditions that place the target peptide in the middle of the 2D chromatogram. This process begins with two scouting gradient elution conditions in the second dimension of a 2D-LC system, followed by building and refining a retention model for the target peptide using a third separation. The process is shown to be generically useful by developing methods for four model peptides, and application to a sample of degraded model peptide to demonstrate its utility for resolving impurities in a real sample. [ABSTRACT FROM AUTHOR]

[Display omitted] • Peptide based dot-blot assay detects AFB1 rapidly, sensitively and is easy-to-use. • Molecular docking of AFB1with human serum albumin generated a specific octapepetide. • Low K d app (323 nM) by indirect ELISA confirmed peptide binding affinity to AFB1. • Dot-blot assay detected AFB1 in food and feed samples and correlated highly to HPLC. • Dot-blot assay is a on-site detection method for safe, healthy food and feed. Aflatoxin B1 (AFB1) is a hepatotoxic and carcinogenic food contaminant. Although on-site paper-based detection is sensitive it depends on expensive antibodies which are difficult to raise against mycotoxins. Here, we rationally designed a high binding octapeptide, N-KSGKSKPR-C peptide for AFB1 detection, by molecular docking, as confirmed by indirect ELISA (K d 323 nM). Further, conjugation of octapeptide with gold nanoparticles (26 nm) permitted its use as a visual detection agent in rapid, sensitive dot-blot assay (LOD 0.39 μg/kg). The assay displayed negligible cross-reactivity with co-contaminating mycotoxins. AFB1 recovery from spiked wheat sample was comparable by dot-blot (78–91 %) and HPLC (65–87 %). Evaluation of dot-blot using certified reference material and 146 food and feed samples showed high correlation R2 = 0.87 with HPLC. The assay displayed high accuracy (91 %), sensitivity (71 %) and specificity (96.5 %). Therefore, the developed dot-blot assay holds promise for monitoring AFB1 contamination in food and feed. [ABSTRACT FROM AUTHOR]

Rice bran has been predominantly used in the feed industry, and only recently it has attracted greater attention in terms of human nutrition with increasing knowledge of its bioactivity. A growing interest is the analysis of physiologically active peptides derived from rice bran proteins. In this paper, the bioactivities of rice bran proteins hydrolysates and peptides are reviewed based on recent studies. These enzymatic hydrolysates and peptides exert various biological activities including antioxidant, antidiabetic, anticancer and inhibitory activity for angiotensin converting enzyme (ACE), which may ultimately prevent certain chronic diseases. Nevertheless, these functionalities can be highly associated with their corresponding structural characteristics, in particular specific sequences and molecular weight distribution. This article may facilitate the expansion of the prospective applications of the bioactive peptides in a number of fields and provide some clues of the relationship between peptides structure and functionality for future research. [ABSTRACT FROM AUTHOR]

There is a growing need in the industrial sector (health, nutrition and cosmetic) to discover new biomolecules with various physico-chemical and bioactive properties. Various beneficial effects of peptides – notably those produced from protein hydrolysis – are reported in the literature. The antioxidant activity involves various mechanisms, among them metal chelation, studied by UV-visible spectrophotometry. In this paper, we set up an original method of screening metal chelating peptides in a hydrolysate using Surface Plasmon Resonance (SPR) for their antioxidant properties. To date, the empirical approach used several cycles of hydrolysate fractionation and bioactivity evaluation until the isolation of the pure bioactive molecule and its identification. Besides, the detection of metal-chelating peptide is not sensitive enough by spectrophotometry. For the first time, metal chelating peptides were screened in hydrolysates using SPR and a correlation was established between affinity constant determined in SPR and metal chelation capacity determined from UV-visible spectrophotometry. [ABSTRACT FROM AUTHOR]

• A supramolecular metallopeptide hydrogel (Supra GHK-Cu) was developed by metal coordination and peptide assembly. • Molecular dynamics simulation indicates the multiple coordination patterns between supramolecular peptides and Cu2+. • Supramolecular metallopeptide showed excellent biostability and wound healing properties. • Supra GHK-Cu exemplifies a successful bio-inspired supramolecular metallopeptide hydrogel. • An alternative strategy to overcome the limitations of traditional bioactive metallopeptides. Inspired by the regulation of protein structure and function by metal ions in life, the role of metal coordination in the folding and assembly of peptides has been gradually studied. However, the construction of bioactive supramolecular metallopeptides with synergism between metal coordination and peptide self-assembly remains challenging. This paper reports a bio-inspired peptide derivative (Supra GHK (glycyl- l -histidyl- l -lysine)) bearing a natural-derived GHK tri-peptide motif, which could self-assemble into supramolecular metallopeptide hydrogel (Supra GHK-Cu) after adding Cu2+. The addition of Cu2+ prompts the allosteric effects on the folded structure of Supra GHK, resulting from the participation of atoms on the backbone of the peptide in the chelation. Cu2+ has a stronger affinity for Supra GHK by bridging two peptide molecules or interacting with one peptide molecule, as confirmed by experimental results and molecular dynamics simulation. Remarkably, due to the formation of supramolecular structures, Supra GHK-Cu possesses excellent resistance against protease degradation. Moreover, it accelerates wound healing more significantly than GHK-Cu by promoting collagen deposition, angiogenesis and cell proliferation. This work not only exemplifies a successful bio-inspired supramolecular metallopeptide hydrogel but also provides a promising alternative strategy to overcome the limitations of traditional bioactive peptides in various biomedical fields. [ABSTRACT FROM AUTHOR]

Peptides are a fast growing segment in the pharmaceutical industry. Consequently, the industry and regulatory agencies are increasing their focus on the regulatory path and quality considerations for peptide development and manufacturing. Although most peptides are synthetic, manufactured by solid phase synthesis, nevertheless they are complex molecules with challenging quality and regulatory aspects. This paper provides a structured overview of relevant quality issues for chemically synthesized peptides used as active pharmaceutical ingredients (API) in drug products. It addresses the unique characteristics of peptides pertaining to structural and physicochemical characterization, manufacturing and in process controls, impurities and aggregates arising from manufacturing and storage, along with their potential impact on safety (including immunogenicity) and efficacy of the peptide drug products. [ABSTRACT FROM AUTHOR]

Phospholipase A 2 (named bitanarin) possessing capability to block nicotinic acetylcholine receptors (nAChRs) was isolated earlier (Vulfius et al., 2011) from puff adder Bitis arietans venom. Further studies indicated that low molecular weight fractions of puff adder venom inhibit nAChRs as well. In this paper, we report on isolation from this venom and characterization of three novel peptides called baptides 1, 2 and 3 that reversibly block nAChRs. To isolate the peptides, the venom of B. arietans was fractionated by gel-filtration and reversed phase chromatography. The amino acid sequences of peptides were established by de novo sequencing using MALDI mass spectrometry. Baptide 1 comprised 7, baptides 2 and 3–10 amino acid residues, the latter being acetylated at the N-terminus. This is the first indication for the presence of such post-translational modification in snake venom proteins. None of the peptides contain cysteine residues. For biological activity studies the peptides were prepared by solid phase peptide synthesis. Baptide 3 and 2 blocked acetylcholine-elicited currents in isolated Lymnaea stagnalis neurons with IC 50 of about 50 μM and 250 μM, respectively. In addition baptide 2 blocked acetylcholine-induced currents in muscle nAChR heterologously expressed in Xenopus oocytes with IC 50 of about 3 μM. The peptides did not compete with radioactive α-bungarotoxin for binding to Torpedo and α7 nAChRs at concentration up to 200 μM that suggests non-competitive mode of inhibition. Calcium imaging studies on α7 and muscle nAChRs heterologously expressed in mouse neuroblastoma Neuro2a cells showed that on α7 receptor baptide 2 inhibited acetylcholine-induced increasing intracellular calcium concentration with IC 50 of 20.6 ± 3.93 μM. On both α7 and muscle nAChRs the suppression of maximal response to acetylcholine by about 50% was observed at baptide 2 concentration of 25 μM, the value being close to IC 50 on α7 nAChR. These data are in accord with non-competitive inhibition as follows from α-bungarotoxin binding experiments. The described peptides are the shortest peptides without disulfide bridges isolated from animal venom and capable to inhibit nAChR by non-competitive way. [ABSTRACT FROM AUTHOR]

HsCen2 displayed different binding modes with three peptides for Kar1p, Rad4 and Sfi1. It reacted with Kar1p through calcium ions and phosphorylation double-regulation. The interaction with Rad4 is only affected by phosphorylation. And for peptide Sfi1, calcium ions or phosphorylation had little effects on their interaction. [Display omitted] • The interaction between centrin and downstream target proteins is regulated by phosphorylation and calcium ions in vitro. • HsCen2 displayed different binding modes with peptides for Kar1p, Rad4 and Sfi1. • The interaction between HsCen2 and Kar1p is regulated by both the binding of calcium ion and phosphorylation of HsCen2. • Phosphorylation modification played main role during HsCen2 binding with Rad4. • Calcium ions or phosphorylation had little effects on HsCen2 interaction with Sfi1. Human centrin 2 (HsCen2) is an important calcium binding protein, which belongs to the conserved EF-hand superfamily. Reversible phosphorylation of protein is a crucial and ubiquitous regulatory mechanism in vivo. In the present paper, we investigated the binding of HsCen2 with the peptides of Kar1p, Rad4 and Sfi1 by isothermal titration calorimetry (ITC), fluorescence spectroscopy and native-PAGE. Based on fluorescence titration and ITC, the conditional dissociation constants of HsCen2 with the peptides were calculated. It is worth noting that HsCen2 displayed different binding modes with these three peptides. It reacted with Kar1p through calcium ions and phosphorylation double-regulation. And phosphorylation modification directed amino acid Ser170 played main role during HsCen2 binding with Rad4. As for peptide Sfi1, calcium ions or phosphorylation modifying Ser170 had little effects on their interaction. The native-PAGE indicated that a new band appeared corresponding to a complex of peptides binding to HsCen2. The binding of HsCen2 to calcium ions and especially phosphorylation of HsCen2 may change the hydrophobic cavities on HsCen2 and result in the changes of interaction of peptides with protein. These results are useful for us to understand the mechanism of phosphorylation regulation function in vivo. [ABSTRACT FROM AUTHOR]

This paper presents formation of a new class of dendritic peptide nanostructures from self-assembly of diphenylalanine extracted from Alzheimer's β-amyloid polypeptide. Effects of different substrates e.g. glass, silicon and gold on morphology of dendritic nanostructures have been studied by means of AFM and FESEM. Furthermore, formation of self-assembled structures in solution has been characterized in terms of dimensions of nanotubes via Zetasizer. The results showed formation of highly ordered dendritic multi-branched structures spread on glass in which diameter of each tubular structure varies from 200 to 800 nm. Silicon substrates promoted aggregation with less dendrite characteristics. Individual nanotubes were formed on gold solid substrates. The growth of nucleation points was accelerated via spin casting. In solution, however, the diameter size showed an average of 296 nm after 1 day of self-assembly. A mechanism is proposed to explain tree-like growth of FF dendritic nanostructures. Our approach offers a biomaterial which proves highly useful for a broad range of application from drug delivery to nanofabrication techniques. [ABSTRACT FROM AUTHOR]

As a further study of Se-containing proteins (Se-Pro) derived from Se-enriched brown rice (Se-BR), this paper aimed to purify and identify Se-containing antioxidative peptides (Se-antioxi-Peps) from Se-Pro hydrolysates. The total Se content in Se-BR was 6.26 μg/g DW, and selenocystine, Se-methylselenocysteine, and selenomethionine were identified as the main organic Se species by high-performance liquid chromatography–inductively coupled plasma mass spectrometry. Se-Pro was extracted and hydrolyzed by four types of proteases, and Alcalase was chosen as the optimum enzyme according to the degree of hydrolysis (DH). The hydrolysate with 17.08% DH possessing the highest DPPH radical scavenging activity was separated into five fractions (F 1 to F 5 ). Fractions F 3 to F 5 , which had high antioxidative activities, were further separated. Sub-fractions F 3-3 , F 4-2 , and F 5-1 were chosen to evaluate antioxidative activities and analyze Se species. The Se-antioxi-Pep with the sequence SeMet-Pro-Ser was identified by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. [ABSTRACT FROM AUTHOR]

This paper reports a strategy to assemble apoptotic cells on a solid surface using a peptide as the recognition element. And a peptide-based electrochemical biosensor to directly evaluate apoptosis is described for the first time. The peptide modified on an electrode is designed to contain the sequence that can recognize externalized phosphatidylserine on apoptotic cells, and can then capture the cells onto the electrode surface. In the electrochemical system, the immobilized cells can not only provide significant steric hindrance for electron transfer, but also shield the positive charges of the peptide that can attract negatively charged electrochemical probes. Therefore, the obtained electrochemical signals drop significantly after the incubation of apoptotic cells, which can be used to reveal the apoptosis level. The experimental results of this approach are well in line with other standard methods. Moreover, this electrochemical method is simple, cost-effective, convenient, sensitive, and holds great potential toward apoptosis evaluation, therapeutic effect assessment and deeper cellular biological studies. [ABSTRACT FROM AUTHOR]

Peptides are a class of protein fragments with relatively high biological activity and intense specificity, which play crucial role in the treatment of Shuxuetong injection (SXT). However, the extraordinary complexity of Chinese medicinal formulates and the lack of systematic identification methods are primary challenges for study of pharmacodynamic peptides. In addition, infinitesimal peptides contents further hinder the identification and structural characterization of polypeptide by traditional means. In this paper, we described a strategy that LC-MS combined with molecular docking to systematically illustrate the peptide components of SXT. The key to this research was used of gene sequencing to establish a SXT protein database to further achieve the separation and enrichment of chemical methods. Moreover, the ADRA2A, PAR4 and DRD3 were precisely docked with the identified peptides. The result indicated that 12 compounds had stable binding ability and were speculated to be the latent bioactive monomers for the treatment of stroke. Additionally, 12 peptides were verified by cell-based experiment. The results showed that only YLKTT could indeed protect astrocytes from oxygen glucose deprivation/reoxygenation (OGD/R). The YLKTT showed higher activity than the others in vitro. It might be a completely new compound that has never been reported before, providing the basis for further research and a new paradigm for stroke. [Display omitted] • Searching active peptides from shuxuetong injection (SXT). • Purpose to protect stroke injury. • Studies involving gene sequencing, docking and cell-based experiment. [ABSTRACT FROM AUTHOR]

Multiple Reaction Monitoring (MRM) conducted on a triple quadrupole mass spectrometer allows researchers to quantify the expression levels of a set of target proteins. Each protein is often characterized by several unique peptides that can be detected by monitoring predetermined fragment ions, called transitions, for each peptide. Concatenating large numbers of MRM transitions into a single assay enables simultaneous quantification of hundreds of peptides and proteins. In recognition of the important role that MRM can play in hypothesis-driven research and its increasing impact on clinical proteomics, targeted proteomics such as MRM was recently selected as the Nature Method of the Year. However, there are many challenges in MRM applications, especially data pre-processing where many steps still rely on manual inspection of each observation in practice. In this paper, we discuss an analysis pipeline to automate MRM data pre-processing. This pipeline includes data quality assessment across replicated samples, outlier detection, identification of inaccurate transitions, and data normalization. We demonstrate the utility of our pipeline through its applications to several real MRM data sets. [ABSTRACT FROM AUTHOR]

Proteinogenic and non-proteinogenic amino acids, fatty acids or glycans are some of the main building blocks of nonribsosomal peptides (NRPs) and as such may give insight into the origin, biosynthesis and bioactivities of their constitutive peptides. Hence, the structural representation of NRPs using monomers provides a biologically interesting skeleton of these secondary metabolites. Databases dedicated to NRPs such as Norine, already integrate monomer-based annotations in order to facilitate the development of structural analysis tools. In this paper, we present rBAN (retro-biosynthetic analysis of nonribosomal peptides), a new computational tool designed to predict the monomeric graph of NRPs from their atomic structure in SMILES format. This prediction is achieved through the "in silico" fragmentation of a chemical structure and matching the resulting fragments against the monomers of Norine for identification. Structures containing monomers not yet recorded in Norine, are processed in a "discovery mode" that uses the RESTful service from PubChem to search the unidentified substructures and suggest new monomers. rBAN was integrated in a pipeline for the curation of Norine data in which it was used to check the correspondence between the monomeric graphs annotated in Norine and SMILES-predicted graphs. The process concluded with the validation of the 97.26% of the records in Norine, a two-fold extension of its SMILES data and the introduction of 11 new monomers suggested in the discovery mode. The accuracy, robustness and high-performance of rBAN were demonstrated in benchmarking it against other tools with the same functionality: Smiles2Monomers and GRAPE. [ABSTRACT FROM AUTHOR]

Purpose: Peptides are gaining significant interests as therapeutic agents due to their high targeting specificity and potency. However, their low bioavailability and short half-lives limit their massive potential as therapeutics. The use of dense, solid particles of biodegradable polymer as a universal carrier for peptides also has its challenges, such as inefficient peptide release and low bioactivity. In this paper, it was established that hollow microparticles (h-MPs) instead of solid microparticles (s-MPs), as peptide carriers, could improve the release efficiency, while better preserving their bioactivity.Methods: Glucagon like Peptide-1 (GLP-1) was encapsulated as a model peptide. Mass loss, average molecular weight changes, intraparticle pH, polymer-peptide interaction and release studies, together with bioactivity assessment of the peptide for s-MPs and h-MPs were systematically analyzed and evaluated for efficacy.Results: The intraparticle pH of s-MPs was as low as 2.64 whereas the pH of h-MPs was 4.99 by day 7. Consequently, 93% of the peptide extracted from h-MPs was still bioactive while only 58% of the peptide extracted from s-MPs was bioactive. Likewise, the cumulative release of GLP-1 by day 14 from h-MPs showed a cumulative amount of 88 ± 8% as compared to 33 ± 6% for s-MPs.Conclusions: The cumulative release of peptide can be significantly improved, and the bioactivity can be better preserved by simply using h-MPs instead of s-MPs as carriers. [ABSTRACT FROM AUTHOR]

The aim of this study was preparation of a soybean protein hydrolyzate with thrombin inhibitory activity and isolation, identification, and characterization of the active peptides from the hydrolyzate. In this study, a soybean protein hydrolyzate with the thrombin inhibiting IC50 value of 2.78 mg/mL was prepared under the improved pepsin hydrolysis condition, which exhibited the highest thrombin inhibitory activity in these soybean protein-derived hydrolyzates. A novel nonapeptide FFPDIPKIK with the IC50 value of 2.36 mM was screened from the hydrolyzate by in silico methods. The kinetic studies and molecular docking showed that the nonapeptide adopted a mixed-type mode to inhibit thrombin and bound with thrombin with several hydrogen bonds and hydrophobic interactions. The nonapeptide was partially digested using the in vitro digestion model, and its truncated peptides had comparable thrombin inhibitory activity. The results suggested that soybean protein hydrolyzate could be exploited as a functional food ingredient against coagulation. [ABSTRACT FROM AUTHOR]