Search

In vitro bioefficacies of the different antimicrobial peptides (AMPs) were tested against three bacteria using paper disc and micro-dilution broth method. Nine different cationic AMPs viz. D4E1, PEP11, ESF1, ESF4, ESF5, ESF6, ESF12, ESF13 and ESF17 exhibiting variable amino acid compositions and charges, were used for the present investigation. Among the various AMPs tested against Xanthomonas axonopodis pv. punicae (Xap), Xanthomonas axonopodis pv. citri (Xac) and Xanthomonas axonopodis pv. malvacearum (Xam), the peptide D4E1 (net charge + 8) was the most effective AMP against all the three Xanthomonas sp. followed by PEP11, ESF12 and ESF1 having net charge +4. The peptide ESF13 was not effective against all the three bacteria while ESF4 was not effective against Xap and Xac whereas ESF6 was also not effective against Xac. AntiMicrobial peptides when tested in vitro through micro-dilution broth method showed that the inhibition growth per cent against Xap was greater than 90% (MIC90) for D4E1, PEP11, ESF17, ESF5 and ESF12. For Xac, D4E1, PEP11, ESF17, ESF5, ESF6, ESF1 and ESF12 showed the inhibition growth percent greater than 90% (MIC90). For Xam, the inhibition growth per cent was seen greater than 90% (MIC90) for D4E1, PEP11, ESF17, ESF1 and ESF12. The most promising peptide D4E1 exhibited better stability against endogenous proteases which recorded only 10.08 % hemolysis at a very high i.e.100 μM concentration. The D4E1 peptides appears to be a promising candidate to be explanted through gene manipulation to control bacterial blight of pomegranate. [ABSTRACT FROM AUTHOR]

Copyright of China Brewing is the property of China Brewing Editorial Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Next-generation single-molecule protein sequencing technologies have the potential to significantly accelerate biomedical research. These technologies offer sensitivity and scalability for proteomic analysis. One auspicious method is fluorosequencing, which involves: cutting naturalized proteins into peptides, attaching fluorophores to specific amino acids, and observing variations in light intensity as one amino acid is removed at a time. The original peptide is classified from the sequence of light-intensity reads, and proteins can subsequently be recognized with this information. The amino acid step removal is achieved by attaching the peptides to a wall on the C-terminal and using a process called Edman Degradation to remove an amino acid from the N-Terminal. Even though a framework (Whatprot) has been proposed for the peptide classification task, processing times remain restrictive due to the massively parallel data acquisicion system. In this paper, we propose a new beam search decoder with a novel state formulation that obtains considerably lower processing times at the expense of only a slight accuracy drop compared to Whatprot. Furthermore, we explore how our novel state formulation may lead to even faster decoders in the future. Author summary: Proteomic analyses frequently rely on mass spectrometry, a method characterized by its limited dynamic range, potentially overlooking low-abundant proteins. To address this limitation, single-molecule protein sequencing methods offer a solution. Fluorosequencing is a cutting-edge single-molecule protein sequencing method, which can distinguish peptides or protein molecules massively parallelly. This method has attracted interest from investors, as evidenced by the recent funding of Erisyon, a company developing this technology. This technique contains a challenging classification task: determining the original peptide sequence from light-intensity observations obtained after several Edman cycles. A classifier based on a combination of k Nearest Neighbors (kNN) with Hidden Markov Models (HMM) had been shown to have close-to-optimal accuracy with tractable complexity. We propose in this paper a new algorithm that reduces computation time significantly at the expense of a slight reduction in accuracy compared to state-of-the-art method. [ABSTRACT FROM AUTHOR]

Antimicrobial resistance, particularly the emergence of resistant strains in fungal pathogens, has become a pressing global health concern. Antifungal peptides (AFPs) have shown great potential as a promising alternative therapeutic strategy due to their inherent antimicrobial properties and potential application in combating fungal infections. However, the identification of antifungal peptides using experimental approaches is time-consuming and costly. Hence, there is a demand to propose fast and accurate computational approaches to identifying AFPs. This paper introduces a novel multi-view feature learning (MVFL) model, called AFP-MVFL, for accurate AFP identification, utilizing multi-view feature learning. By integrating the sequential and physicochemical properties of amino acids and employing a multi-view approach, the AFP-MVFL model significantly enhances prediction accuracy. It achieves 97.9%, 98.4%, 0.98, and 0.96 in terms of accuracy, precision, F1 score, and Matthews correlation coefficient (MCC), respectively, outperforming previous studies found in the literature. [ABSTRACT FROM AUTHOR]

During their biosynthesis, Sonic hedgehog (Shh) morphogens are covalently modified by cholesterol at the C-terminus and palmitate at the N-terminus. Although both lipids initially anchor Shh to the plasma membrane of producing cells, it later translocates to the extracellular compartment to direct developmental fates in cells expressing the Patched (Ptch) receptor. Possible release mechanisms for dually lipidated Hh/Shh into the extracellular compartment are currently under intense debate. In this paper, we describe the serum-dependent conversion of the dually lipidated cellular precursor into a soluble cholesteroylated variant (ShhC) during its release. Although ShhC is formed in a Dispatched- and Scube2-dependent manner, suggesting the physiological relevance of the protein, the depalmitoylation of ShhC during release is inconsistent with the previously postulated function of N-palmitate in Ptch receptor binding and signaling. Therefore, we analyzed the potency of ShhC to induce Ptch-controlled target cell transcription and differentiation in Hh-sensitive reporter cells and in the Drosophila eye. In both experimental systems, we found that ShhC was highly bioactive despite the absence of the N-palmitate. We also found that the artificial removal of N-terminal peptides longer than eight amino acids inactivated the depalmitoylated soluble proteins in vitro and in the developing Drosophila eye. These results demonstrate that N-depalmitoylated ShhC requires an N-peptide of a defined minimum length for its signaling function to Ptch. [ABSTRACT FROM AUTHOR]

Honey is a natural product that is used by a large number of people because of its distinctive compositional constituents, which have a considerable impact on its market value. The distinctive combination of amino acids and sugars found in honey's composition, along with its peptide content, could potentially provide several benefits to human health. During the past few years, cutting-edge techniques have been developed and used for the purpose of investigating, identifying, and characterizing peptides that are produced from honey bees. Therefore, the purpose of this review is to examine current trends and technological advancements in the study of honey bee-derived peptides, focusing on innovative and cutting-edge methods. Furthermore, this review explores various attributes of honey and its components, including the honey bee-derived peptide defensin-1. In addition, this review investigates various methods for separating and purifying peptides, as well as the factors that affect these methods. Additionally, defensin-1, a peptide produced by honey bees, is discussed along with its antioxidant and antimicrobial capabilities. In addition, this review focuses on cutting-edge and innovative omic methods used to study honey bee peptides, as well as the significance of artificial intelligence tools in their investigation. Consequently, the review paper delves into various significant obstacles faced by researchers and scientists studying honey bee peptides, while also offering an extensive range of fascinating opportunities and possibilities for future research for those interested in groundbreaking discoveries in this area. [ABSTRACT FROM AUTHOR]

Anticancer peptides (ACPs) are short protein sequences; they perform functions like some hormones and enzymes inside the body. The role of any protein or peptide is related to its structure and the sequence of amino acids that make up it. There are 20 types of amino acids in humans, and each of them has a particular characteristic according to its chemical structure. Current machine and deep learning models have been used to classify ACPs problems. However, these models have neglected Amino Acid Repeats (AARs) that play an essential role in the function and structure of peptides. Therefore, in this paper, ACPs offer a promising route for novel anticancer peptides by extracting AARs based on N-Grams and k-mers using two peptides' datasets. These datasets pointed to breast and lung cancer cells assembled and curated manually from the Cancer Peptide and Protein Database (CancerPPD). Every dataset consists of a sequence of peptides and their synthesis and anticancer activity on breast and lung cancer cell lines. Five different feature selection methods were used in this paper to improve classification performance and reduce the experimental costs. After that, ACPs were classified using four classifiers, namely AdaBoost, Random Forest Tree (RFT), Multi-class Support Vector Machine (SVM), and Multi-Layer Perceptron (MLP). These classifiers were evaluated by applying five well-known evaluation metrics. Experimental results showed that the breast and lung ACPs classification process provided an accurate performance that reached 89.25% and 92.56%, respectively. In terms of AUC, it reached 95.35% and 96.92% for both breast and lung ACPs, respectively. The proposed classifiers performed competently somewhat equally in AUC, accuracy, precision, F-measures, and recall, except for Multi-class SVM-based feature selection, which showed superior performance. As a result, this paper significantly improved the predictive performance that can effectively distinguish ACPs as virtual inactive, experimental inactive, moderately active, and very active. [ABSTRACT FROM AUTHOR]

Peptide identification from tandem mass spectrometry data is a fundamental task in computational proteomics. Traditional algorithms perform well when facing unmodified peptides. However, when peptides have post-translational modifications (PTMs), these methods cannot provide satisfactory results. Recently, open search methods have been proposed to identify peptides with PTMs. While the performance of these new methods is promising, the identification results vary greatly with respect to the quality of tandem mass spectra and the number of PTMs in peptides. This motivates us to systematically study the relationship between the performance of open search methods and the quality parameters of tandem mass spectrometry data as well as the number of PTMs in peptides. In this paper, we have proposed an analytical model derived from simulated data to describe the relationship between the probability of obtaining correct results and the spectrum quality as well as the number of PTMs. The proposed model is verified using 1,464,146 real experimental spectra. The consistent trend observed in both simulated data and real data reveals the necessary conditions to effectively apply open search methods. Source code of our study is available at http://bioinformatics.ust.hk/PST.html. [ABSTRACT FROM AUTHOR]

Fluorescence indicators capable of binding to human immunodeficiency virus-1 (HIV-1) trans-activation responsive (TAR) RNA are powerful tools for the exploratory studies of the identification of anti-HIV drug candidates. This work presents a new design strategy for fluorogenic indicators with a transactivator of transcription (Tat)-derived peptide based on the forced intercalation of thiazole orange (TO) dyes (FIT). The developed 9-mer FIT peptide (RKKRR-TO-RRR: named FiLuP) features the TO unit integrated onto a Dap (2,3-diaminopropionic acid) residue in the middle of the Tat peptide sequence; the Q (glutamic acid) residue in the Tat peptide (RKKRR-Q-RRR) is replaced with TO as if it were an amino acid surrogate. This facilitates a significant light-up response (450-fold at λem = 541 nm, Φfree = 0.0057, and Φbound = 0.61) upon binding to TAR RNA. The response of FiLuP is highly selective to TAR RNA over other non-cognate RNAs, and FiLuP maintains strong binding affinity (Kd = 1.0 ± 0.6 nM). Significantly, in contrast to previously developed Tat peptide-based FRET probes, FiLuP is able to discriminate between "competitive" and "noncompetitive" inhibitors when used in the fluorescence indicator displacement (FID) assay. The FID assay under stringent screening conditions is also possible, enabling super-strong competitive binders toward TAR RNA to be sieved out. [ABSTRACT FROM AUTHOR]

Context: The paper considers the features of the structure and dipole moments of several amino acids and their dipeptides which play an important role in the formation of the peptide nanotubes based on them. The influence of the features of their chirality (left L and right D) and the alpha-helix conformations of amino acids are taken into account. In particular, amino acids with aromatic rings, such as phenylalanine (Phe/F), and branched-chain amino acids (BCAAs)—leucine (Leu/L) and isoleucine (Ile/I)—as well as corresponding dipeptides (diphenylalanine (FF), dileucine (LL), and diisoleucine (II)) are considered. The main features and properties of these dipeptide structures and peptide nanotubes (PNTs), based on them, are investigated using computational molecular modeling and quantum-chemical semi-empirical calculations. Their polar, piezoelectric, and photoelectronic properties and features are studied in detail. The results of calculations of dipole moments and polarization, as well as piezoelectric coefficients and band gap width, for different types of helical peptide nanotubes are presented. The calculated values of the chirality indices of various nanotubes are given, depending on the chirality of the initial dipeptides—the results obtained are consistent with the law of changes in the type of chirality as the hierarchy of molecular structures becomes more complex. The influence of water molecules in the internal cavity of nanotubes on their physical properties is estimated. A comparison of the results of these calculations by various computational methods with the available experimental data is presented and discussed. Method: The main tool for molecular modeling of all studied nanostructures in this work was the HyperChem 8.01 software package. The main approach used here is the Hartree–Fock (HF) self-consistent field (SCF) with various quantum-chemical semi-empirical methods (AM1, PM3, RM1) in the restricted Hartree–Fock (RHF) and in the unrestricted Hartree–Fock (UHF) approximations. Optimization of molecular systems and the search for their optimal geometry is carried out in this work using the Polak–Ribeire algorithm (conjugate gradient method), which determines the optimized geometry at the point of their minimum total energy. For such optimized structures, dipole moments D and electronic energy levels (such as EHOMO and ELUMO), as well as the band gap Eg = ELUMO − EHOMO, were then calculated. For each optimized molecular structure, the volume was calculated using the QSAR program implemented also in the HyperChem software package. [ABSTRACT FROM AUTHOR]

A green strategy for the selective alkylation of cysteine-containing peptides in a continuous flow reactor has been developed, providing an efficient pathway to alkylated cysteine-containing peptides under mild conditions. This process does not need light, metal catalysts, or oxidative reagents. It provides a useful method for the modification of amino acids and peptides. As one of the low cost and synthetic versatile raw materials, the alkyl thianthenium salt can be used as an alkylation source in the preparation of alkylated cysteine-containing peptides. In addition, the microfluidics technology can shorten the reaction time and improve the efficiency, thus reducing the costs and energy consumption of the synthesis process. A series of alkylated cysteine-containing peptides (41 examples) has been synthesized here with a short residence time (14.0 min), and with good to excellent yields. [ABSTRACT FROM AUTHOR]

Insufficient research on the material basis and functional product development of horse bones has led to the waste of resources. This paper, as the by-product of horse meat bone marrow was the object, aimed to discover the flavor and antioxidant activity of novel collagen peptides. Two peptides, HBMP-1-1 and HBMP-2-1, were isolated and purified from horse bone marrow collagen protein (HBMP) hydrolysates. The combination of spectroscopic and chromatographic methods including SDS-PAGE, UV, FT-IR, CD, and SEM identified the structures of the peptides. The amino acid composition, flavor characteristics, and antioxidant activity were also evaluated. SDS-PAGE analysis showed that the molecular weight of the two peptides was concentrated under 4.1 kDa. The total amino acid contents of the HBMP-1-1 was up to 570.779 mg/g. Leucine, alanine, and glutamicacid were the predominant amino acids in HBMP-1-1 with high nutritional value, and it contained 10.07% β-folding, 46.39% β-turn, and 43.54% random coil structure. The peptide sequences IDDPTDSKPE, LNGKLTGM, ELDEGYVPK, AFQEDPDKF, and FVGKVVDPTQK with molecular weights of 1116.51, 833.45, 1049.51, 1096.49, and 1217.69 Da were detected using LC-MS/MS. The results of the antioxidant activity test showed that separation and purification significantly improved the bioactivity of the protein. The half-inhibition rate of HBMP-1-1 against DPPH, ABTS, and hydroxyl radicals were 0.054, 0.050, and 0.137 mg/mL, respectively. This article provides a scientific basis for clarifying the material basis of horse bone marrow collagen peptides. Also, it provides new approaches and ideas for exploring efficient and safe bone-derived lead compounds and products. [ABSTRACT FROM AUTHOR]

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/. [ABSTRACT FROM AUTHOR]

Context: The inhibitory effect of asparagine (Asn) and its derivatives on iron (Fe) corrosion was studied by performing density functional theory (DFT) calculations. In this paper, the global and local reactivity descriptors of Asn in the protonated and neutral forms were evaluated. Also, the changes in reactivity were investigated when dipeptides were combined with Asn. Due to the increase in the reaction centers within their molecular structure, there was an enhancement in the inhibitory effect of these dipeptides. Moreover, the adsorption energies (Eads) and the adsorption configurations of Asn and small peptides (SPs) with most stability were determined on the surface of Fe(111). It was found that dipeptides had a chemical adsorption on these substrates. In the protonated forms, there was an enhancement in the absolute values of Eads between the inhibitors and the Fe(111) surfaces. Peptides were more likely to be adsorbed on the Fe surfaces, showing the great inhibitory effect of these moieties. The results of the current research demonstrate the possibility of utilizing SPs as efficient "green" corrosion inhibitors. Methods: DFT computations were undertaken by employing the BIOVIA Material Studio with B3LYP-D3 functional and 6–31 + G* basis set. The theoretical evaluation of the inhibitory effect of asparagine (Asn) dipeptides, and the potential analysis of small peptides to protect against the corrosion of Fe, was done. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

In this paper we study two lysine-based peptide dendrimers with Lys-His-Arg and Lys-Arg-His repeating units and terminal lysine groups. Combination of His and Arg properties in a dendrimer could be important for biomedical applications, especially for prevention of dendrimer aggregation and for penetration of dendrimers through various cell membranes. We describe the synthesis of these dendrimers and the confirmation of their structure using 1D and 2D Nuclear Magnetic Resonance (NMR) spectroscopy. NMR spectroscopy and relaxation are used to study the structural and dynamic properties of these macromolecules and to compare them with properties of previously studied dendrimers with Lys-2Arg and Lys-2His repeating units. Our results demonstrate that both Lys-His-Arg and Lys-Arg-His dendrimers have pH sensitive conformation and dynamics. However, properties of Lys-His-Arg at normal pH are more similar to those of the more hydrophobic Lys-2His dendrimer, which has tendency towards aggregation, while the Lys-Arg-His dendrimer is more hydrophilic. Thus, the conformation with the same amino acid composition of Lys-His-Arg is more pH sensitive than Lys-Arg-His, while the presence of Arg groups undoubtedly increases its hydrophilicity compared to Lys-2His. Hence, the Lys-His-Arg dendrimer could be a more suitable (in comparison with Lys-2His and Lys-Arg-His) candidate as a pH sensitive nanocontainer for drug delivery. [ABSTRACT FROM AUTHOR]

Cancer is one of the main diseases threatening human life, accounting for millions of deaths around the world each year. Traditional physical and chemical methods for cancer treatment are extremely time-consuming, lab-intensive, expensive, inefficient and difficult to be applied in a high-throughput way. Hence, it is an urgent task to develop automated computational methods to enable fast and accurate identification of anticancer peptides (ACPs). In this paper, we develop a novel model named iACP-GE to identify ACPs. Multi-features are extracted by using binary encoding, enhanced grouped amino acid composition and BLOSUM62 encoding based on the N5C5 sequence, as well as detrended forward moving-average auto-cross correlation analysis based on physicochemical properties of 20 natural amino acids. Thus, 835 features are obtained for each sample, in order to avoid information redundancy, gradient boosting decision tree was adopted as the feature selection strategy. Then, the optimal feature subset is input to the extra tree classifier. The accuracies of ACP740 and ACP240 datasets with the 5-fold cross-validation were 90.54% and 91.25%, respectively. Experimental results indicate that iACP-GE significantly outperforms several existing models on ACP740 and ACP240 datasets and can be used as an effective tool for the identification of ACPs. The datasets and source codes for iACP-GE are available at . [ABSTRACT FROM AUTHOR]

Synthetic therapeutic peptides are a complex and popular class of pharmaceuticals. In recent years, peptides with proven therapeutic activity have gained significant interest in the market. The determination of synthetic peptide enantiomeric purity plays a critical role in the evaluation of the quality of the medicine. Since racemization is one of the most common side reactions occurring in AAs or peptides, enantiomeric impurities such as D‐isomers can form during the peptide synthesis or can be introduced from the starting materials (e.g., AAs). The therapeutic effect of a synthetic or semi‐synthetic bioactive peptide molecule depends on its AA enantiomeric purity and secondary/tertiary structure. Therefore, the enantiomeric purity determination for synthetic peptides is supportive for interpreting unwanted therapeutic effects and determining the quality of synthetic peptide therapeutics. However, enantiomeric purity analysis encounters formidable analytical challenges during chromatographic separation, as D/L isomers have identical physical–chemical properties except stereochemical configuration. To ensure peptides AA stereochemical configuration whether in the free or bound state, sensitive and reproducible quantitative analytical method is mandatory. In this regard, numerous analytical techniques were emerged for the quantification of D‐isomeric impurities in synthetic peptides, but still, very few reports are available in the literature. Thus, the purpose of this paper is to provide an overview of the importance, regulatory requirements, and various analytical methods used for peptide enantiomeric purity determination. In addition, we discussed the available literature in terms of enantiomeric impurity detection, common hydrolysis procedural aspects, and different analytical strategies used for sample preparation. [ABSTRACT FROM AUTHOR]

Recent scientific evidence indicates that protein hydrolysates contain bioactive peptides that have potential benefits for human health. However, the bitter‐tasting hydrophobic peptides in protein hydrolysates negatively affect the sensory quality of resulting products and limit their utilization in food and pharmaceutical industries. The approaches to reduce, mask, and remove bitter taste from protein hydrolysates have been extensively reported. This review paper focuses on the advances in the knowledge regarding the structure–bitterness relationship of peptides, the release mechanism of bitter peptides, and the debittering methods for protein hydrolysates. Bitter tastes generating with enzymatic hydrolysis of protein is influenced by the type, concentration, and bitter taste threshold of bitterness peptides. A "bell‐shaped curve" is used to describe the relationship between the bitterness intensity of the hydrolysates and the degree of hydrolysis. The bitter receptor perceives bitter potencies of bitter peptides by the hydrophobicity recognition zone. The intensity of bitterness is influenced by hydrophobic and electronic properties of amino acids and the critical spatial structure of peptides. Compared to physicochemical debittering (i.e., selective separation, masking of bitter taste, encapsulation, Maillard reaction, and encapsulation) and other biological debittering (i.e., enzymatic hydrolysis, enzymatic deamidation, plastein reaction), enzymatic hydrolysis is a promising debittering approach as it combines protein hydrolyzation and debittering into a one‐step process, but more work should be done to advance the knowledge on debittering mechanism of enzymatic hydrolysis and screening of suitable proteases. Further study can focus on combining physicochemical and biological approaches to achieve high debittering efficiency and produce high‐quality products. [ABSTRACT FROM AUTHOR]

The N-capping region of an α-helix is a short N-terminal amino acid stretch that contributes to nucleate and stabilize the helical structure. In the VEGF mimetic helical peptide QK, the N-capping region was previously demonstrated to be a key factor of QK helical folding. In this paper, we explored the effect of the chiral inversion of the N-capping sequence on QK folding, performing conformational analysis in solution by circular dichroism and NMR spectroscopy. The effect of such a modification on QK stability in serum and the proliferative effect were also evaluated. [ABSTRACT FROM AUTHOR]

Despite the fact that peptide conjugates with a pendant ferrocenyl (Fc) have been widely investigated, bis-ferrocenyl end-capped peptides are rarely synthetized. In this paper, in addition to the full characterization of the Fc-CO-[L-Dap(Boc)]n-NH-Fc series, we report a comparison of the three series of bis-ferrocenyl homopeptides synthesized to date, to gain insights into the influence of α-amino isobutyric (Aib), 2,3-diamino propionic (Dap) and Cα,β-didehydroalanine (ΔAla) amino acids on the peptide secondary structure and on the ferrocene redox properties. The results obtained by 2D NMR analysis and X-ray crystal structures, and further supported by electrochemical data, evidence different behaviors depending on the nature of the amino acid; that is, the formation of 310-helices or fully extended (2.05-helix) structures. In these foldamers, the orientation of the carbonyl groups in the peptide helix yields a macrodipole with the positive pole on the N-terminal amino acid and the negative pole on the C-terminal amino acid, so that oxidation of the Fc moieties takes place more or less easily depending on the orientation of the macrodipole moment as the peptide chain grows. Conversely, the fully extended conformation adopted by ΔAla flat peptides neither generates a macrodipole nor affects Fc oxidation. The utilization as electrochemical and optical (Circular Dichroism) probes of the two terminal Fc groups, bound to the same peptide chain, makes it possible to study the end-to-end effects of the positive charges produced by single and double oxidations, and to evidence the presence "exciton-coupled" CD among the two intramolecularly interacting Fc groups of the L-Dap(Boc) series. [ABSTRACT FROM AUTHOR]

Copyright of Shipin Kexue/ Food Science is the property of Food Science Editorial Department and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Particular interest has been focused on the modulation of solid state charge transport in proteins via π–π interactions. Nevertheless, molecular design with the π–π interaction mode for electronic applications remains a challenge in light of the complexity of protein structures. Here, we investigate the pattern of regulating peptide charge transport via different types of π–π interactions in peptide-based frameworks. We applied aromatic amino acid containing peptides labelled with a 1-methyl-1′-aminoethyl-4,4′-bipyridinium salt (MV2+) to construct well-defined self-assembled monolayers as the model. When the π–π interactions are improved by the size of aromatic amino acid side chains, the peptide charge transport can be promoted mainly by the reduced energy barrier and not by the weakened peptide−electrode coupling. When the π–π interactions are attenuated rapidly by increasing the distance between aromatic groups, the molecule–electrode coupling is enhanced sharply, which becomes the main factor to facilitate the charge transport. [ABSTRACT FROM AUTHOR]

Cardiovascular diseases (CVD) are a significant and growing burden on global health services, and it is now accepted that impairment of vascular function represents a major preliminary step in the development of CVD. There is considerable interest in identifying both causal factors of impaired vascular function, as well as related nutritional factors that may lower the risk of developing CVD, and food‐derived bioactive peptides and amino acids have emerged as one such area. Dairy foods contain two groups of proteins, whey proteins and caseins, which represent a rich source of bioactive peptides that are released during food processing and/or digestion. These peptides have a number of physiological activities including the potential to reduce blood pressure. Research, including acute and longer‐term randomised controlled trials, animal models and in vitro models has demonstrated the potential impact of dairy proteins on vascular function. The purpose of this paper is to narratively review the evidence, primarily from randomised controlled trials, examining the effects of whey proteins, their peptides and amino acids on vascular function and related issues including blood pressure. In addition, it will explore the potential underlying mechanisms responsible for these effects. It concludes that there is increasing evidence that whey proteins, and notably the bioactive peptides and amino acids released during their digestion, can have beneficial effects on aspects of vascular function and thus contribute to CVD risk reduction. It also highlights a number of beneficial effects of whey proteins including those on blood pressure, arterial stiffness, nitric oxide production and inflammation. [ABSTRACT FROM AUTHOR]

Introduction: The MHC‐peptide interaction has a subtle influence on host resistance to virus. This paper aims to study the relationship between MHC‐peptide interaction and MHC‐related virus‐resistance. Methods: By 3D homology modeling, the structure of chicken BF2 molecule BF2*0201 (PDB code: 4d0d) was studied and compared with the known structures of BF2 molecule BF2*0401 (PDB code: 4e0r) to elucidate the characteristics of BF2*0201‐binding antigenic peptides. Results: The results show that due to the amino acid difference between the two binding groove of 4e0r and 4d0d, the size of the binding groove of the two are 1130 ų and1380 ų respectively, indicating the amino acid species that 4e0r binding peptide has lower selectivity than 4d0d; and because of large side chain conformation of Arg (especially Arg111) of 4e0r replaced by small side chain Tyr111 of 4d0d, the volume of central part of the binding groove of 4d0d is obviously larger than that of 4e0r, indicating that the restrictive of binding antigenic peptides for 4d0d is narrower than that of 4e0r; and on account of the chargeability of the binding groove of the two are different, namely the binding groove chargeability of 4e0r (strong positive polarity) and 4d0d (weak negative polarity). Conclusion: There are generally more peptides presented by the BF2 of B2 haplotype than by that of B4 haplotype, leading to more resistance of B2 than that of B4 to virus. [ABSTRACT FROM AUTHOR]

Copyright of Modern Food Science & Technology is the property of Editorial Office of Modern Food Science & Technology and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Recently, we presented a strategy for packaging peptides as side‐chains in high‐density brush polymers. For this globular protein‐like polymer (PLP) formulation, therapeutic peptides were shown to resist proteolytic degradation, enter cells efficiently and maintain biological function. In this paper, we establish the role charge plays in dictating the cellular uptake of these peptide formulations, finding that peptides with a net positive charge will enter cells when polymerized, while those formed from anionic or neutral peptides remain outside of cells. Given these findings, we explored whether cellular uptake could be selectively induced by a stimulus. In our design, a cationic peptide is appended to a sequence of charge‐neutralizing anionic amino acids through stimuli‐responsive cleavable linkers. As a proof‐of‐concept study, we tested this strategy with two different classes of stimuli, exogenous UV light and an enzyme (a matrix metalloproteinase) associated with the inflammatory response. The key finding is that these materials enter cells only when acted upon by the stimulus. This approach makes it possible to achieve delivery of the polymers, therapeutic peptides or an appended cargo into cells in response to an appropriate stimulus. [ABSTRACT FROM AUTHOR]

Baijiu is a traditional Chinese distilled beverage. There are twelve types of Chinese baijiu, each requiring different production technologies resulting in varying styles and characteristics. Proteins, peptides and amino acids are both sources of nitrogen for brewing microflora and precursors of flavour compounds. These compounds are the main non‐volatile nitrogenous compounds in baijiu fermentation but are also present in the final product. Of the volatile nitrogenous compounds in baijiu, pyrazines dominate. This paper reviews the roles of nitrogenous compounds in baijiu production; systematically summarises the volatile and non‐volatile nitrogenous compounds in baijiu and the relationships between production processes and nitrogenous compounds in Strong and Sauce flavour baijiu. Nitrogenous compounds are closely related to the quality of the baijiu. It is suggested that future work should focus on the role of nitrogenous compounds in the flavour and aroma of baijiu with particular regard to different production technologies, materials and regions. © 2022 The Institute of Brewing & Distilling [ABSTRACT FROM AUTHOR]

In this paper, four models of quantitative structure-activity relationship (QSAR) for 84 angiotensin I-converting enzyme inhibitory (ACEI) dipeptides, 169 ACEI tripeptides and 15 ACEI tetrapeptides and the total 268 peptides were established, respectively. During every modeling process, the structure of the peptides were firstly described using a set of amino acid descriptor SVHEHS proposed previously in our laboratory, then QSAR models were developed successfully by orthogonal signal correction combined with support vector machine (OSC-SVM). Furthermore, all models were validated by the reasonable statistical parameters, such as correlation coefficient (R2), cross-validated correlation coefficient (q2) and external validation coefficient (q2ext), etc. The results demonstrated that all developed QSAR models had excellent fitting accuracy and predictive ability. It could be a very promising approach for QSAR study on bioactive peptides using SVHEHS descriptor and OSC-SVM. [ABSTRACT FROM AUTHOR]

Microcin C7 (McC) as a viable form of antimicrobial has gained substantial attention due to its distinctive antimicrobial activity, by targeting aspartyl tRNA synthetase. McC can be a potential solution against pathogenic microbial infections in the postantibiotic era. However, considering that degradation by digestive enzymes can disrupt the function of this peptide in the gastrointestinal tract, in this study, we attempt to design McC variants to overcome several barriers that may affect its stability and biological activity. The mccA gene encoding the McC peptide precursor was mutated and 12 new McC variants with trypsin resistance were found. The Yej+rimL− strain was used as an indicator to determine the minimum inhibitory concentrations (MICs). The results showed that three variants, including R2A, R2T and R2Q, among 12 variants formed by the replacement of the second arginine of the McC peptide with different amino acids, were resistant to trypsin and had an outstanding antimicrobial ability, with MIC values of 12.5, 25, and 25 μg/mL, respectively. Taken together, our findings show that the engineering of the site-directed mutagenesis of McC significantly enhances McC trypsin resistance and maintains a great antimicrobial activity. [ABSTRACT FROM AUTHOR]

Self-assembling peptides are of huge interest for biological, medical and nanotechnological applications. The enormous chemical variety that is available from the 20 amino acids offers potentially unlimited peptide sequences, but it is currently an issue to predict their supramolecular behavior in a reliable and cheap way. Herein we report a computational method to screen and forecast the aqueous self-assembly propensity of amyloidogenic pentapeptides. This method was found also as an interesting tool to predict peptide crystallinity, which may be of interest for the development of peptide based drugs. [ABSTRACT FROM AUTHOR]

Seed proteins, especially those of amaranth, are characterized using different peptides with important biological functions. The aim of this work is to describe, at a theoretical–experimental level, the selective separation of encrypted peptides with high-added value. The interactions between amino acid–PAMAM and peptide–PAMAM were determined using quantum chemistry and instrumental techniques of structural analysis, with the obtained results showing correlation between both methods of identification and characterization. The molecular properties of amino acids, peptides (models) and PAMAM were determined using density functional theory (DFT), specifically B3LYP and the 6-31G(d,p) basis set. The synthesis of the dendrimer (PAMAM) was carried out by optimizing the traditional process to reduce cost and waste generation. The analysis of the vibrational frequencies between tyrosine and PAMAM using the DFT method correlated satisfactorily with the experimental data. The interaction energy of the most stable complexes was between those of the first generation PAMAM dendrimer, the amino acid tyrosine and the PAMAMAM–YLAGKPQQEH peptide, with a value of −31.25 kcal mol−1 and −27.19 kcal mol−1, respectively. Likewise, the molecular electrostatic potential map and the intermolecular hydrogen bonds allowed visualizing the interactions between the captured atoms (amino acids and peptides) and the synthesized PAMAM. This work showed evidence at the molecular level of selectivity of encrypted oligopeptides. The theoretical study was determined to define the types of peptides that could interact with PAMAM after enzymatic hydrolysis, as well as the type of interaction, and the atoms involved in the formation of a dendrimer–peptide complex. Subsequently, at the experimental level, these residues were mapped by mass spectrometry in a MALDI-TOF detector, having results that can be homologated with the theoretical results. This study opens the door to novel studies for the separation of bioactive peptides. [ABSTRACT FROM AUTHOR]

In the past 20 years, the global per capita protein demand has been increasing year by year, and thus the search for sustainable and healthier alternative proteins is the focus of current food research. Yeast proteins are of microbial origin with environmentally friendly advantages. They are high-quality proteins with high bioavailability and are expected to be used as novel alternative proteins for food applications. Although reports on yeast extracts continue to increase, studies on the composition, production methods, and functional properties of yeast proteins lack systematic reviews. In addition, the application of yeast proteins in the food industry has not been summarized previously. This paper reviews the composition of yeast proteins and the approaches for their isolation and extraction, and systematically introduces the functional properties and the wide applications in food fields. Future perspectives for yeast proteins to sustainably and healthily meet the world's growing protein demand are also elucidated. Yeast proteins have great application potential as alternative proteins with a reasonable proportion of amino acid composition. Yeast proteins can be hydrolyzed to produce yeast peptides and can also be used as protein supplements, fining agents, meat extenders, etc. Overcoming the limitations of high nucleic acid content and high cost, and improving the functional properties and sensory acceptability of yeast proteins will greatly promote their market applications. This review will provide ideas and guidance for the research and development of yeast proteins in food applications. Yeast proteins have high nutritional value with an ideal amino acid composition and a wealth of functions and properties. The excellent characteristics allow yeast proteins to be used as sustainable alternative proteins in food applications. [Display omitted] • The compositions and extraction approaches of yeast proteins are overviewed. • The functional properties of yeast proteins are summarized. • The applications of yeast proteins as alternative proteins in food are reviewed. • The strategies to improve the utilization of yeast proteins are emphasized. [ABSTRACT FROM AUTHOR]

The alteration of amino acid register in peptides could affect their folding properties and thus functions. The effect of sequence in metal ion induced folding of peptide/protein is important in the design of new functional protein structures, such as biomimetics. In this paper, a set of hairpin peptides with identical composition but different histidine locations have been designed to exploit the metal ion‐mediated peptide intramolecular folding transformation through the adjustment of histidine and lysine residue locations. The results demonstrated that the histidine positions in peptide sequence could dramatically affect the coordination modes between peptides and Cu(II) ion. The Cu(II) coordination could affect the secondary structure transformation and self‐assembly along with electrostatic interaction and hydrogen bonding synergistically. Three molecules with VHVH sequence at each side of the turn segment (VDPPT) were apt to coordinate with Cu(II) ion with three or four histidines. The closer the VHVH motifs were to the turn segment, the more easier the molecules were to form β sheet structure with the promotion of Cu(II) ions. These results demonstrated that the purposeful location of key amino acids in peptides could achieve the controllable conformation transformation of hairpin peptides, which provides useful strategies for biomimetic design, such as metalloenzymes. [ABSTRACT FROM AUTHOR]

Terahertz spectroscopy and density functional theory (DFT) calculations have been used to study the dipeptide l-carnosine. In this paper, we expand the range of materials described with THz measurements and DFT calculations from amino acids to dipeptides. Three clear resonances were detected in the experimental spectrum at 1.5 THz, 1.9 THz, and 2.3 THz. Additionally, we performed periodic boundary condition DFT calculations. The computational spectrum accurately reproduces the experimental one. [ABSTRACT FROM AUTHOR]

Copyright of Journal of Chinese Institute of Food Science & Technology is the property of Journal of Chinese Institute of Food Science & Technology Periodical Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

The reliable identification and quantitation of phosphorylated amino acids, peptides and proteins is one of the key challenges in contemporary bioanalytical research, an area of particular interest when attempting to diagnose and treat diseases at an early stage. We have developed a synthetic probe for targeting phosphorylated amino acids, based on core–shell submicron-sized particles consisting of a silica core, coated with a molecularly imprinted polymer (MIP) shell. The MIP layer contains a fluorescent probe crosslinker which binds selectively to phosphorylated tyrosine (pY) moieties with a significant imprinting factor (IF) and responds with a "light-up" fluorescence signal. The bead-based ratiometric detection scheme has been successfully transferred to a microfluidic chip format and its applicability to rapid assays has been exemplarily shown by discriminating a pY-terminating oligopeptide against its non-phosphorylated counterpart. Such miniaturised devices could lead to an automated pY or pY N-terminated peptide measurement system in the future. The setup combines a modular microfluidic system for amino acid derivatisation, extraction (by micropillar co-flow) and selective adsorption and detection with the fluorescent MIP core–shell particle probes. A miniaturised optical assembly for low-light fluorescence measurements was also developed, based on miniaturised opto-electronic parts and optical fibres. The emission from the MIP particles upon binding of pY or pY N-terminated peptides could be monitored in real-time. [ABSTRACT FROM AUTHOR]

Copyright of MESO is the property of Zadruzna Stampa D.D. and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Shipin Kexue/ Food Science is the property of Food Science Editorial Department and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

The liquid-liquid phase separation of biopolymers in living cells contains multiple interactions and occurs in a dynamic environment. Resolving the regulation mechanism is still a challenge. In this work, we designed a series of peptides (XXLY)6SSSGSS and studied their complexation and coacervation behavior with single-stranded oligonucleotides. The "X" and "Y" are varied to combine known amounts of charged and non-charged amino acids, together with the introduction of secondary structures and pH responsiveness. Results show that the electrostatic interaction, which is described as charge density, controls both the strength of complexation and the degree of chain relaxation, and thus determines the growth and size of the coacervates. The hydrophobic interaction is prominent when the charges are neutralized. Interestingly, the secondary structures of peptides exhibit profound effect on the morphology of the phases, such as solid phase to liquid phase transition. Our study gains insight into the phase separation under physiological conditions. It is also helpful to create coacervates with desirable structures and functions. [ABSTRACT FROM AUTHOR]

A DNA cassette assembly method is described which utilizes inexpensive oligomers no longer than 40 nt in length. The five-segment cassettes have 20 nt overlaps which give an effective length of 80 nt, making it possible to code for peptides up to 20 amino acids long. The cassettes have three phosphate free nicks, which can be successfully inserted into plasmid DNA and used to transform E. coli. The nicks are repaired in vivo by an unknown mechanism. Insertions are not successful for cassettes with greater than three nicks. A procedure is provided for rapid turnaround from DNA design to peptides, which are easily isolated as C-terminal fusions with GFP. The technique generally gives the expected sequence, with errors which occur about 1% of the time. Several representative DNA inserts are described which illustrate the method, as well as chemical details on the new peptides coded for. The peptides can be readily mutated to make it possible to understand how polar and aromatic residues affect GFP-fusion solubility, and how histidine residues can be strategically placed in a peptide for good IMAC retention. The method can be used to explore a large number of new designed peptides as fusion products quickly and economically. [ABSTRACT FROM AUTHOR]

The biological and technological importance of anion-mediated processes has made the development of improved methods for the selective recognition of anions one of the most relevant research topics today. The hydration sphere of anions plays an important role in the functions performed by anions by forming a variety of cluster complexes. Here we describe a supramolecular capsule that recognizes hydrated anion clusters. These clusters are most likely composed of three ions that form hydrated C3 symmetry complexes that are entrapped within the supramolecular capsule of the same symmetry. The capsule is made of self-assembled α,γ-cyclic peptide containing amino acid with by five-membered rings and equipped with a tris(triazolylethyl)amine cap. To recognise the hydrated anion clusters, the hexapeptide capsule must disassemble to entrap them between its two subunits. Due to the biological and technological importance of anion-mediated processes, the development of selective recognition methods which account for the hydration sphere of anions is highly relevant. Here, the authors describe a supramolecular capsule that recognizes hydrated anion clusters by disassembling to trap them between its two subunits. [ABSTRACT FROM AUTHOR]

Small peptides (SPs), ranging from 5 to 100 amino acids, play integral roles in plants due to their diverse functions. Despite their low abundance and small molecular weight, SPs intricately regulate critical aspects of plant life, including cell division, growth, differentiation, flowering, fruiting, maturation, and stress responses. As vital mediators of intercellular signaling, SPs have garnered significant attention in plant biology research. This comprehensive review delves into SPs' structure, classification, and identification, providing a detailed understanding of their significance. Additionally, we summarize recent findings on the biological functions and signaling pathways of prominent SPs that regulate plant growth and development. This review also offers a perspective on future research directions in peptide signaling pathways. [ABSTRACT FROM AUTHOR]

Self‐assembling peptides have numerous applications in medicine, food chemistry, and nanotechnology. However, their discovery has traditionally been serendipitous rather than driven by rational design. Here, HydrogelFinder, a foundation model is developed for the rational design of self‐assembling peptides from scratch. This model explores the self‐assembly properties by molecular structure, leveraging 1,377 self‐assembling non‐peptidal small molecules to navigate chemical space and improve structural diversity. Utilizing HydrogelFinder, 111 peptide candidates are generated and synthesized 17 peptides, subsequently experimentally validating the self‐assembly and biophysical characteristics of nine peptides ranging from 1–10 amino acids—all achieved within a 19‐day workflow. Notably, the two de novo‐designed self‐assembling peptides demonstrated low cytotoxicity and biocompatibility, as confirmed by live/dead assays. This work highlights the capacity of HydrogelFinder to diversify the design of self‐assembling peptides through non‐peptidal small molecules, offering a powerful toolkit and paradigm for future peptide discovery endeavors. [ABSTRACT FROM AUTHOR]

Natural antimicrobial peptides (AMPs) and enzymes (AMEs) are promising non-antibiotic candidates against antimicrobial resistance but suffer from low efficiency and poor stability. Here, we develop peptide nanozymes which mimic the mode of action of AMPs and AMEs through de novo design and peptide assembly. Through modelling a minimal building block of IHIHICI is proposed by combining critical amino acids in AMPs and AMEs and hydrophobic isoleucine to conduct assembly. Experimental validations reveal that IHIHICI assemble into helical β-sheet nanotubes with acetate modulation and perform phospholipase C-like and peroxidase-like activities with Ni coordination, demonstrating high thermostability and resistance to enzymatic degradation. The assembled nanotubes demonstrate cascade antifungal actions including outer mannan docking, wall disruption, lipid peroxidation and subsequent ferroptotic death, synergistically killing >90% Candida albicans within 10 min on disinfection pad. These findings demonstrate an effective de novo design strategy for developing materials with multi-antimicrobial mode of actions. Natural antimicrobial peptides and enzymes are good candidates for application but suffer from low stability. Here, the authors report on biomimetic self-assembling peptides which mimic both antimicrobial peptide and enzyme functionality, demonstrating application against fungal infection. [ABSTRACT FROM AUTHOR]

Copyright of Food Research & Development is the property of Food Research & Development Editorial Department and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

We aimed to develop an amino acid sequence-dependent analytical method using near-infrared (NIR) spectroscopy. The detailed analysis of the NIR spectra of eight different amino acid aqueous solutions (glycine, alanine, serine, glutamine, lysine, phenylalanine, tyrosine, and proline) revealed different spectral patterns characteristic of different amino acid residues in the 6200–5700 and 5000–4200 cm−1 regions, and the amino acids were identified based on the patterns. The spectra in the region of 5000–4500 cm−1 for tripeptide organic solutions that were composed of the aforementioned eight amino acids clearly showed the spectral differences depending on the amino acid species and amino acid sequences. Namely, tripeptide species were clearly differentiated from each other based on the spectral pattern of NIR bands due to the combinations of N–H stretching and amide II/III modes and those derived from the first overtones of amide II and amide I. The quantitative evaluation of changes in the concentrations of dipeptides and tripeptides composed of two different amino acids, glycine and proline was performed using partial least squares regression (PLSR) analysis and a combination of bands for amide modes. The calibration and validation results with high determination coefficients (R2 ≥ 0.99) were successfully obtained based on the amino acid sequences. The results not only revealed the usefulness of NIR spectroscopy as a process analytical technology (PAT) tool for synthesizing peptides in a micro flow reactor but also proposed a general method for quantitatively analyzing NIR spectra obtained in the course of chemical synthesis. [ABSTRACT FROM AUTHOR]

A scoring function plays a critical role in software for peptide identification with mass spectrometry. We present a general scoring feature that can be incorporated in the scoring functions of other peptide identification software. The scoring feature is based on the intensity ratios between two adjacent y-ions in the spectrum. A method is proposed to obtain the probability distributions of such ratios, and to calculate the scoring feature based on the distributions. To demonstrate the performance of the method, the new feature is incorporated with X!Tandem , and Novor and significantly improved the database search and de novo sequencing performances on the testing data, respectively. [ABSTRACT FROM AUTHOR]

In the preceding paper, using ECEPP, including the effects of water, and the chain build-up procedure, we computed the low energy structures for GnRH and found that there were no distinct low energy structures or structures with high statistical weights. To attempt to deduce possible structures of GnRH that may bind to the GnRH receptor, we computed the low energy structures for GnRH peptides that have l- and d-amino acids substituting for Gly 6. The l-amino acid-substituted peptides ( l-Ala and l-Val) have very low or no affinity for the receptor and on activity (release of FSH and LH) while the d-Ala-, d-Leu-, d-Trp- and d-Phe-substituted peptides have significantly higher relative affinities and activities than those for native GnRH; the d-Val-substituted peptide has about one-third of the affinity and activity as native GnRH. Unlike native GnRH, our computations suggest that both sets of peptides form well-defined structures in water: the l-amino acid-substituted peptides are predominantly α-helical while the d-amino acid-substituted peptides adopted E*A A A E D*(C*) A E C A(C*) and minor variants of these structures. By eliminating structures that lay in common to the d-Ala and l-Val peptides and further eliminating structures that differed between the d-Ala and d-Leu peptides, we reduced the number of possible distinct binding conformations to 254. Searching for structures among these 254 conformations that had relative statistical weights that paralleled their relative affinities, we found two candidate structures: D*E A A E C*A E C A and D*G A A E D*A E C G*, both of which have conformations for residues 3-9 that are similar to the computed most probable structures for the d-amino acid-substituted GnRH peptides in water. [ABSTRACT FROM AUTHOR]

Phototriggers are useful molecular tools to initiate reactions in enzymes by light for the purpose of photoenzymatic design and mechanistic investigations. Here, we incorporated the non-natural amino acid 5-cyanotryptophan (W5CN) in a polypeptide scaffold and resolved the photochemical reaction of the W5CN–W motif using femtosecond transient UV/Vis and mid-IR spectroscopy. We identified a marker band of ∼2037 cm−1 from the CN stretch of the electron transfer intermediate W5CN·− in the transient IR measurement and found UV/Vis spectroscopic evidence for the W·+ radical at 580 nm. Through kinetic analysis, we characterized that the charge separation between the excited W5CN and W occurs in 253 ps, with a charge-recombination lifetime of 862 ps. Our study highlights the potential use of the W5CN–W pair as an ultrafast phototrigger to initiate reactions in enzymes that are not light-sensitive, making downstream reactions accessible to femtosecond spectroscopic detection. [ABSTRACT FROM AUTHOR]