Sequence Analysis Of Peptides Research Articles

Proteome Profiling of Cucurbita pepo Phyllosphere After Infection by Podosphaera xanthii and Application of Reynoutria sachalinensis Extract

Podosphaera xanthii is the main causal agent of powdery mildew (PM) disease for Cucurbita pepo. Disease control is attained principally by applications of chemical fungicides, along with parallel use of tolerant crop varieties and alternate application of elicitors to control development of disease resistance. To get insight into C. pepo molecular responses to P. xanthii infection and elicitor treatment we studied the proteomic profile differences at the phyllosphere of a zucchini cultivar susceptible to PM, at the onset of P. xanthii (PX) infection and after application of Reynoutria sachalinensis (RS) plant extract, respectively, using a nano-LC-HRMS/MS, Q-Exactive-Orbitrap approach. Analysis of peptide sequences regarding four treatment groups (Control; PX; RS; and RSPX (PX-infected priorly treated with RS)) resulted in 2070 CuGenDB annotations. Three comparisons (treatments vs. Control) encompassed most of the Differentially Expressed Proteins (DEPs). In these three comparisons, KEGG and Gene Ontology functional analyses highlighted unique differentially enriched pathways—some of which included highly expressed proteins—in PX-related (proteasome, pentose phosphate pathway, and carbon fixation), RS-related (biosynthesis of secondary metabolites, flavonoids, and starch and sucrose metabolism), and RSPX-related (pyruvate metabolism and polycomb repressive complex) comparisons, respectively, suggesting distinct mechanisms of early plant responses modulated by PX and RS. Furthermore, in four out of six comparisons the thiamine metabolism pathway was found to be enriched, suggesting a pivotal role in PX-induced responses.

The Hunt Lab Guide to De Novo Peptide Sequence Analysis by Tandem Mass Spectrometry

Donald Hunt has made seminal contributions to the fields of proteomics, immunology, epigenetics, and glycobiology. The foundation of every important work to come out of the Hunt Laboratory is de novo peptide sequencing. For decades, he taught hundreds of students, postdocs, engineers, and scientists to directly interpret mass spectral data. To honor his legacy and ensure that the art of de novo sequencing is not lost, we have adapted his teaching materials into “The Hunt Lab Guide to De Novo Peptide Sequence Analysis by Tandem Mass Spectrometry”. In addition to the de novo sequencing tutorials, we present two freely available software tools that facilitate manual interpretation of mass spectra and validation of search results. The first, “Hunt Lab Peptide Fragment Calculator”, calculates precursor and fragment mass-to-charge ratios for any peptide. The second program, “Predator Protein Fragment Calculator”, was inspired in part by the fragment calculator developed in the Hunt Lab. Its capabilities are enhanced to facilitate interpretation of mass spectral data derived from intact proteins. We hope that the combination of these educational tools will continue to benefit students and researchers by empowering them to interpret data on their own.

Discovery of Lacto-N-Biosidases and a Novel N-Acetyllactosaminidase Activity in the CAZy Family GH20: Functional Diversity and Structural Insights.

The glycoside hydrolase family 20 (GH20) predominantly features N-acetylhexosaminidases (EC 3.2.1.52), with only few known lacto-N-biosidases (EC 3.2.1.140; LNBases). LNBases catalyze the degradation of lacto-N-tetraose (LNT), a prominent component of human milk oligosaccharides, thereby supporting a healthy infant gut microbiome development. We investigated GH20 diversity to discover novel enzymes that release disaccharides such as lacto-N-biose (LNB). Our approach combined peptide clustering, sequence analysis, and 3D structure model evaluation to assess active site topologies, focusing on the presence of a subsite -2. Five LNBases were active on pNP-LNB and four showed activity on LNT. One enzyme displayed activity on both pNP-LacNAc and pNP-LNB, establishing the first report of N-acetyllactosaminidase (LacNAcase) activity. Exploration of this enzyme cluster led to the identification of four additional enzymes sharing this dual substrate specificity. Comparing the determined crystal structure of a specific LNBase (TrpyGH20) and the first crystal structure of an enzyme with dual LacNAcase/LNBase activity (TrdeGH20) revealed a highly conserved subsite -1, common to GH20 enzymes, while the -2 subsites varied significantly. TrdeGH20 had a wider subsite -2, accommodating Gal with both β1,4- and β1,3-linkages to the GlcNAc in subsite -1. Biotechnological applications of these enzymes may include structural elucidation of complex carbohydrates and glycoengineering.

Stem-Cell-Regenerative and Protective Effects of Squid (Symplectoteuthis oualaniensis) Skin Collagen Peptides against H2O2-Induced Fibroblast Injury.

Recently, there has been a growing interest in collagen peptides derived from marine sources for their notable ability to protect skin cells against apoptosis induced by oxidants. Therefore, the current study aimed to investigate the fundamental properties of collagen peptides, including their physicochemical, thermal, structural, stem-cell-regenerative, and skin-cell-protective effects, in comparison to commercial collagen peptides. The acid-soluble (ASC) and pepsin-soluble (PSC) collagens exhibited three distinct bands on SDS-PAGE, namely α (α1 and α2), β, and γ chains, confirming a type I pattern. The thermal profiles obtained from TG and DSC analyses confirmed the denaturation of PSC and ASC at temperatures ranging from 51.94 to 56.4 °C and from 52.07 to 56.53 °C, respectively. The purified collagen peptides were analyzed using SDS-PAGE and MALDI-TOF mass spectrometry, revealing a mass range of 900-15,000 Da. Furthermore, the de novo peptide sequence analysis confirmed the presence of the Gly-X-Y repeating sequence in collagen peptides. Collagen peptide treatments significantly enhanced HFF-1 cell proliferation and migration compared to the control group. ELISA results confirmed the potential interactions between collagen peptides and HFF-1 cells through α2β1, α10β1, and α11β1 integrin receptors. Notably, collagen peptide treatment effectively restored the proliferation of HFF-1 cells damaged by H2O2. Consequently, the advantageous characteristics of squid skin collagen peptides highlight their promising role in regenerative medicine.

Anti-methicillin-resistant Staphylococcus aureus and antibiofilm activity of new peptides produced by a Brevibacillus strain.

Methicillin-resistant Staphylococcus aureus (MRSA) is listed as a highly prioritized pathogen by the World Health Organization (WHO) to search for effective antimicrobial agents. Previously, we isolated a soil Brevibacillus sp. strain SPR19 from a botanical garden, which showed anti-MRSA activity. However, the active substances were still unknown. The cell-free supernatant of this bacterium was subjected to salt precipitation, cation exchange, and reversed-phase chromatography. The antimicrobial activity of pure substances was determined by broth microdilution assay. The peptide sequences and secondary structures were characterized by tandem mass spectroscopy and circular dichroism (CD), respectively. The most active anti-MRSA peptide underwent a stability study, and its mechanism was determined through scanning electron microscopy, cell permeability assay, time-killing kinetics, and biofilm inhibition and eradication. Hemolysis was used to evaluate the peptide toxicity. The pure substances (BrSPR19-P1 to BrSPR19-P5) were identified as new peptides. Their minimum inhibition concentration (MIC) and minimum bactericidal concentration (MBC) against S. aureus and MRSA isolates ranged from 2.00 to 32.00 and 2.00 to 64.00 µg/mL, respectively. The sequence analysis of anti-MRSA peptides revealed a length ranging from 12 to 16 residues accompanied by an amphipathic structure. The physicochemical properties of peptides were predicted such as pI (4.25 to 10.18), net charge at pH 7.4 (-3 to +4), and hydrophobicity (0.12 to 0.96). The CD spectra revealed that all peptides in the water mainly contained random coil structures. The increased proportion of α-helix structure was observed in P2-P5 when incubated with SDS. P2 (NH2-MFLVVKVLKYVV-COOH) showed the highest antimicrobial activity and high stability under stressed conditions such as temperatures up to 100 °C, solution of pH 3 to 10, and proteolytic enzymes. P2 disrupted the cell membrane and caused bacteriolysis, in which its action was dependent on the incubation time and peptide concentration. Antibiofilm activity of P2 was determined by which the half-maximal inhibition of biofilm formation was observed at 2.92 and 4.84 µg/mL for S. aureus TISTR 517 and MRSA isolate 2468, respectively. Biofilm eradication of tested pathogens was found at the P2 concentration of 128 µg/mL. Furthermore, P2 hemolytic activity was less than 10% at concentrations up to 64 µg/mL, which reflected the hemolysis index thresholds of 32. Five novel anti-MRSA peptides were identified from SPR19. P2 was the most active peptide and was demonstrated to cause membrane disruption and cell lysis. The P2 activity was dependent on the peptide concentration and exposure time. This peptide had antibiofilm activity against tested pathogens and was compatible with human erythrocytes, supporting its potential use as an anti-MRSA agent in this post-antibiotic era.

Recent developments in capillary and microchip electroseparations of peptides (2021-mid-2023).

This review article brings a comprehensive survey of developments and applications of high-performance capillary and microchip electromigration methods (zone electrophoresis in a free solution or in sieving media, isotachophoresis, isoelectric focusing, affinity electrophoresis, electrokinetic chromatography, and electrochromatography) for analysis, micropreparation, and physicochemical characterization of peptides in the period from 2021 up to ca. the middle of 2023. Progress in the study of electromigration properties of peptides and various aspects of their analysis, such as sample preparation, adsorption suppression, electroosmotic flow regulation, and detection, are presented. New developments in the particular capillary electromigration methods are demonstrated, and several types of their applications are reported. They cover qualitative and quantitative analysis of synthetic or isolated peptides and determination of peptides in complex biomatrices, peptide profiling of biofluids and tissues, and monitoring of chemical and enzymatic reactions and physicochemical changes of peptides. They include also amino acid and sequence analysis of peptides, peptide mapping of proteins, separation of stereoisomers of peptides, and their chiral analyses. In addition, micropreparative separations and physicochemical characterization of peptides and their interactions with other (bio)molecules by the above CE methods are described.

DeepTAP: An RNN-based method of TAP-binding peptide prediction in the selection of tumor neoantigens

The transport of peptides from the cytoplasm to the endoplasmic reticulum (ER) by transporters associated with antigen processing (TAP) is a critical step in the intracellular presentation of cytotoxic T lymphocyte (CTL) epitopes. The development and application of computational methods, especially deep learning methods and new neural network strategies that can automatically learn feature representations with limited knowledge, provide an opportunity to develop fast and efficient methods to identify TAP-binding peptides. Herein, this study presents a comprehensive analysis of TAP-binding peptide sequences to derive TAP-binding motifs and preferences for N-terminal and C-terminal amino acids. A novel recurrent neural network (RNN)-based method called DeepTAP, using bidirectional gated recurrent unit (BiGRU), was developed for the accurate prediction of TAP-binding peptides. Our results demonstrated that DeepTAP achieves an optimal balance between prediction precision and false positives, outperforming other baseline models. Furthermore, DeepTAP significantly improves the prediction accuracy of high-confidence neoantigens, especially the top-ranked ones, making it a valuable tool for researchers studying antigen presentation processes and T-cell epitope screening. DeepTAP is freely available at https://github.com/zjupgx/deeptap and https://pgx.zju.edu.cn/deeptap.

Abstract B070: Global proteomics and phosphoproteomics profiling of prostate cancer patient derived xenografts tumors from the LuCaP series

Abstract Castration Resistant Prostate Cancer (CRPC) is a form of prostate cancer (PCa) that is resistant to androgen deprivation therapies. Resistance to these therapies leads to metastatic CRPC of adenocarcinoma (AD) origin and can transform to emergent aggressive variant prostate cancer (AVPC) which has genetic aberration features similar to neuroendocrine (NE) phenotypes. Understanding and identifying the underlying mechanisms of resistance and genetic transformations leading to protein alterations will enable us to develop novel therapeutic methods to counteract this resistance and improve outcomes for men with lethal metastatic prostate cancer. To this end, we used patient-derived xenografts (PDXs), an in-vivo clinically relevant model from advanced prostate cancer (PC) patients, to investigate the biology, identify novel protein targets and evaluate new treatment modalities. We aimed to identify known and novel protein kinase targets that might be phospho-regulated unique between CRPC, in AD and AVPC in NE. To pursue this, we applied a mass spectrometry base phosphoproteomics analysis. We processed 48 PDX samples, which included 15 non-castrated (NCR), 18 castration resistant (CR), which are the AD samples and 15 AVPC, the NE tumors. To enrich for global phosphorylated residues, we used sequential metal oxide affinity chromatography. We sequenced peptides from each sample using liquid chromatography in tandem with Orbitrap Eclipse Tribid MS and FAIMS technology for 2 hour gradients. To normalize and calibrate the LC method and to compare across all 48 runs, we spiked-in 400 femtomol of internal standards (iRT) to each sample. For peptide sequence and search analysis, we used Maxquant search algorithm. Using a > 0.75 probability phospho-residue cut-off and 5% FDR, we identified more than 9,700 phospho-residues. We identified RET, ASCL1, CHGA and SYP in NEPC and Androgen Receptor (AR), FOXA1, HOXB13, NKX3.1 and TACSTD2 in the adenocarcinoma PDX LuCap tumor samples, which confirms that our approach detected specific proteins already previously established. We subsequently performed a kinase substrate enrichment analysis and identified GSK-3, ERK1, ERK2, CDK5 kinases to be significantly enriched in the NE tumors while ATM kinase and PKC alpha and beta were enriched in the AD PDX tumor samples. Hierarchical clustering analysis across NE versus AD tumor samples indicated that samples within each group clustered uniquely where we observed intra and inter sample variability. We generated pathway enrichment and GSEA analysis, identified novel targets for therapeutic treatments and novel surface proteins. In conclusion, we have performed a global mass spectrometry based proteomic analysis and created an important first global phosphoproteomics and proteomics database that provides insights into the differentially regulated protein and phosphoproteins between AD and NE PDX tumors and provide a protein database source to develop new hypothesis. Citation Format: Zoi E. Sychev, Gabbrianne E. Larson, Hannah E. Bergom, Abderrahman E. Day, Megan E. Ludwig, Atef E. Ali, Eva Corey, Stephen R. Plymate, Justin E. Hwang, Justin M. Drake. Global proteomics and phosphoproteomics profiling of prostate cancer patient derived xenografts tumors from the LuCaP series [abstract]. In: Proceedings of the AACR Special Conference: Advances in Prostate Cancer Research; 2023 Mar 15-18; Denver, Colorado. Philadelphia (PA): AACR; Cancer Res 2023;83(11 Suppl):Abstract nr B070.

Isolation, Identification, and Biological Activity Analysis of Swim Bladder Polypeptides from Acipenser schrencki.

Swim bladder polypeptides (SBPs) of Acipenser schrencki were analyzed for their antioxidant activity and physicochemical properties. The results showed the optimal enzymatic conditions were alkaline protease with a solid-to-liquid ratio of 1:20, an incubation time of 4 h, a temperature of 55 °C, and an enzyme dosage of 5000 U/g. Three different molecular weight fractions (F1, F2, and F3) were obtained via ultrafiltration. F3 (912.44-2135.82 Da) showed 77.90%, 72.15%, and 66.25% removal of O2•-, DPPH•, and •OH, respectively, at 10 mg/mL, which was significantly higher than the F1 and F2 fractions (p < 0.05). F3 contained proline (6.17%), hydroxyproline (5.28%), and hydrophobic amino acids (51.39%). The UV spectrum of F3 showed maximum absorption at 224 nm. Peptide sequence analysis showed that F3 contained antioxidant peptides (MFGF, GPPGPRGPPGL, and GPGPSGERGPPGPM) and exhibited inhibitory activities on angiotensin-converting enzyme and dipeptidyl peptidase III/IV (FRF, FPFL and LPGLF). F3 was considered a good raw material for obtaining bioactive peptides.

Isobaric Stable Isotope N‐Phosphorylation Labeling (iSIPL) for Ultrasensitive Proteome Quantification

AbstractStable isotope chemical labeling methods have been widely used for high‐throughput mass spectrometry (MS)‐based quantitative proteomics in biological and clinical applications. However, the existing methods are far from meeting the requirements for high sensitivity detection. In the present study, a novel isobaric stable isotope N‐phosphorylation labeling (iSIPL) strategy was developed for quantitative proteome analysis. The tryptic peptides were selectively labeled with iSIPL tag to generate the novel reporter ions containing phosphoramidate P−N bond with high intensities under lower collision energies. iSIPL strategy are suitable for peptide sequencing and quantitative analysis with high sensitivity and accuracy even for samples of limited quantity. Furthermore, iSIPL coupled with affinity purification and mass spectrometry was applied to measure the dynamics of cyclin dependent kinase 9 (CDK9) interactomes during transactivation of the HIV‐1 provirus. The interaction of CDK9 with PARP13 was found to significantly decrease during Tat‐induced activation of HIV‐1 gene transcription, suggesting the effectiveness of iSIPL strategy in dynamic analysis of protein‐protein interaction in vivo. More than that, the proposed iSIPL strategy would facilitate large‐scale accurate quantitative proteomics by increasing multiplexing capability.

Isobaric Stable Isotope N-Phosphorylation Labeling (iSIPL) for Ultrasensitive Proteome Quantification.

Stable isotope chemical labeling methods have been widely used for high-throughput mass spectrometry (MS)-based quantitative proteomics in biological and clinical applications. However, the existing methods are far from meeting the requirements for high sensitivity detection. In the present study, a novel isobaric stable isotope N-phosphorylation labeling (iSIPL) strategy was developed for quantitative proteome analysis. The tryptic peptides were selectively labeled with iSIPL tag to generate the novel reporter ions containing phosphoramidate P-N bond with high intensities under lower collision energies. iSIPL strategy are suitable for peptide sequencing and quantitative analysis with high sensitivity and accuracy even for samples of limited quantity. Furthermore, iSIPL coupled with affinity purification and mass spectrometry was applied to measure the dynamics of cyclin dependent kinase 9 (CDK9) interactomes during transactivation of the HIV-1 provirus. The interaction of CDK9 with PARP13 was found to significantly decrease during Tat-induced activation of HIV-1 gene transcription, suggesting the effectiveness of iSIPL strategy in dynamic analysis of protein-protein interaction in vivo. More than that, the proposed iSIPL strategy would facilitate large-scale accurate quantitative proteomics by increasing multiplexing capability.

MatchTope: A tool to predict the cross reactivity of peptides complexed with Major Histocompatibility Complex I.

The therapeutic targeting of the immune system, for example in vaccinology and cancer treatment, is a challenging task and the subject of active research. Several in silico tools used for predicting immunogenicity are based on the analysis of peptide sequences binding to the Major Histocompatibility Complex (pMHC). However, few of these bioinformatics tools take into account the pMHC three-dimensional structure. Here, we describe a new bioinformatics tool, MatchTope, developed for predicting peptide similarity, which can trigger cross-reactivity events, by computing and analyzing the electrostatic potentials of pMHC complexes. We validated MatchTope by using previously published data from in vitro assays. We thereby demonstrate the strength of MatchTope for similarity prediction between targets derived from several pathogens as well as for indicating possible cross responses between self and tumor peptides. Our results suggest that MatchTope can enhance and speed up future studies in the fields of vaccinology and cancer immunotherapy.

Sequence Analysis and Molecule Docking of Collagenase Inhibitory Peptides from the Peptic Hydrolysate of Flounder Skin

Sequence Analysis and Molecule Docking of Collagenase Inhibitory Peptides from the Peptic Hydrolysate of Flounder Skin

ACE-inhibitory activities of peptide fractions (

In this study, the effects of five adjunct lactobacilli on the formation of angiotensin-converting enzyme inhibitory (ACE-i) peptides in model cheeses were investigated. A total of seven peptide fractions (less than 3 kDa) were obtained by means of a fraction collector coupled with a HPLC system. ACE-i activity and peptide sequence analysis of the seven fractions were determined by RP-HPLC and then MALDI-ToF-MS techniques, respectively. Peptides produced from αs1- and κ-caseins had higher amounts compared to those produced by other caseins. There were considerable differences between the fractions in terms of peptide sequences and ACE-i activities. In general, the peptide fraction containing Lactobacillus delbrueckii ssp. bulgaricus exhibited a higher level of ACE-i activity (79.56%) than the other samples. The next highest ACE-i activity was determined in the cheese containing L. plantarum and significant differences were observed between the ACE-i activities of the fractions. The highest ACE-i activity was identified in fractions including f1 (51.39%) for L. casei, f6 (33.49%) for L. helveticus, f4 (46.62%) for L. helveticus DPC4571 and f1 (47.96%) for cheese containing non-adjunct culture. In conclusion, use of lactobacilli as an adjunct in model cheese increased the peptide types and amounts and also ACE-i activity.

Data From “A Biocodicological Analysis of the Medieval Library and Archive From Orval Abbey, Belgium”

The dataset contains the first-ever comprehensive biocodicological analysis of medieval library books and charters using Zooarchaeological Mass Spectrometry (ZooMS). Here, we analyze 68 codices and 59 charters (1490+59 samples in total) from one single monastic institution, namely the Cistercian abbey of Orval in present-day Belgium. The data entails both peptide mass fingerprinting (using MALDI-ToF) and peptide sequencing (using LC-MS/MS) analysis of almost the entire library and all the preserved single leaf charters from the monastery. MALDI-ToF data is stored in Zenodo – a multidisciplinary open access repository while the LC-MS/MS data is deposited in ProteomeXchange Consortium via PRIDE – a publicly available repository for MS-based proteomics data. Mass spectrometric data generated from an entire monastic library and archive is of immense value to integrate with multiple case studies aiming at understanding parchment production and use in medieval Europe. Paper linked with data: Ruffini-Ronzani, N., Nieus, J.F., Soncin, S., Hickinbotham, S., Dieu, M., Bouhy, J., Charles, C., Ruzzier, C., Falmagne, T., Hermand, X., Collins, M.J. and Deparis, O 2021. A biocodicological analysis of the medieval library and archive from Orval Abbey, Belgium. <em>Royal Society Open Science, 8</em>(6), p.210210.

OKN-007 Alters Protein Expression Profiles in High-Grade Gliomas: Mass Spectral Analysis of Blood Sera

Current therapies for high-grade gliomas, particularly glioblastomas (GBM), do not extend patient survival beyond 16–22 months. OKN-007 (OKlahoma Nitrone 007), which is currently in phase II (multi-institutional) clinical trials for GBM patients, and has demonstrated efficacy in several rodent and human xenograft glioma models, shows some promise as an anti-glioma therapeutic, as it affects most aspects of tumorigenesis (tumor cell proliferation, angiogenesis, migration, and apoptosis). Combined with the chemotherapeutic agent temozolomide (TMZ), OKN-007 is even more effective by affecting chemo-resistant tumor cells. In this study, mass spectrometry (MS) methodology ESI-MS, mass peak analysis (Leave One Out Cross Validation (LOOCV) and tandem MS peptide sequence analyses), and bioinformatics analyses (Ingenuity® Pathway Analysis (IPA®)), were used to identify up- or down-regulated proteins in the blood sera of F98 glioma-bearing rats, that were either untreated or treated with OKN-007. Proteins of interest identified by tandem MS-MS that were decreased in sera from tumor-bearing rats that were either OKN-007-treated or untreated included ABCA2, ATP5B, CNTN2, ITGA3, KMT2D, MYCBP2, NOTCH3, and VCAN. Conversely, proteins of interest in tumor-bearing rats that were elevated following OKN-007 treatment included ABCA6, ADAMTS18, VWA8, MACF1, and LAMA5. These findings, in general, support our previous gene analysis, indicating that OKN-007 may be effective against the ECM. These findings also surmise that OKN-007 may be more effective against oligodendrogliomas, other brain tumors such as medulloblastoma, and possibly other types of cancers.

Regulation of skeletal muscle AMP deaminase. Carbethoxylation of His-51 belonging to the zinc coordination sphere of the rabbit enzyme promotes its desensitization towards the inhibition by ATP

BackgroundSkeletal muscle AMP deaminase (AMPD1) regulates the concentration of adenine nucleotides during muscle contraction. We previously provided evidence that rabbit AMPD1 is composed by two HPRG 73 kDa subunits and two 85 kDa catalytic subunits with a dinuclear zinc site with an average of two histidine residues at each metal site. AMPD1 is mainly expressed in fast twitching fibers and is inhibited by ATP. The limited trypsinization of the 95-residue N-terminal domain of rabbit AMPD1 desensitizes the enzyme towards ATP inhibition at the optimal pH 6.5, but not at pH 7.1. MethodsThe modified residues of rabbit AMPD1 after incubation with radioactive diethyl pyrocarbonate ([14C]DEP) causing the desensitization to inhibition by ATP at pH 7.1 have been identified by sequence analysis and MS analysis of the radioactive peptides liberated from the carbethoxylated enzyme by limited proteolysis with trypsin. ResultsThe study confirms the presence of a dinuclear zinc site in rabbit AMPD1 and shows that carbethoxylation of His-51 at the N-terminus of the catalytic subunit removes the inhibition of the enzyme by ATP at pH 7.1. ConclusionsThe desensitization to ATP is due to the modification of His-51 of the Zn2 coordination sphere which is transduced in a conformational change of the enzyme C-terminus, where an ATP-binding site has been localized. General significanceThe progress in the study of the complex regulation of rabbit AMPD1 that shares an identical amino acid sequence with the human enzyme is important in relation to the role of the enzyme during mammalian evolution.

Characterization, Biological Activity, and Mechanism of Action of a Plant-Based Novel Antifungal Peptide, Cc-AFP1, Isolated From Carum carvi.

Due to the increasing rate of invasive fungal infections and emerging antifungal resistance, development of novel antifungal drugs has been an urgent necessity. Antifungal peptides (AFPs) have recently attracted attention due to their unique ability to evade drug-resistant fungal pathogens. In this study, a novel AFP, Cc-AFP1, with a molecular weight of ~3.759 kDa, was isolated from Carum carvi L., purified by ammonium sulfate precipitation and reversed-phase HPLC and finally identified by sequence analysis using Edman degradation. Peptide sequence analysis revealed a fragment of 36 amino acid residues as RVCFRPVAPYLGVGVSGAVRDQIGVKLGSVYKGPRG for Cc-AFP1 with a net charge of +5 and a hydrophobicity ratio of 38%. The antifungal activity of Cc-AFP1 was confirmed against Aspergillus species with MIC values in the range of 8–16 µg/ml. Cc-AFP1 had less than 5% hemolytic activity at 8–16 µg/ml on human red blood cells with no obvious cytotoxicity against the HEK293 cell line. Stability analysis showed that the activity of Cc-AFP1 was maintained at different temperatures (20°C to 80°C) and pH (8 to 10). The results of a propidium iodide uptake and transmission electron microscopy showed that the antifungal activity of Cc-AFP1 could be attributed to alteration in the fungal cell membrane permeability. Taken together, these results indicate that Cc-AFP1 may be an attractive molecule to develop as a novel antifungal agent combating fungal infections cause by Aspergillus species.

Identification and characterization of antioxidant peptides obtained from the bioaccessible fraction of α-lactalbumin hydrolysate.

Whey is an abundantand sustainable source of bioactive peptides obtained from cheese making process. Whey proteins such as α-lactalbumin can be biologically active when the bioactive peptides encrypted in the amino acid sequence of the native protein are released by enzymatic hydrolysis. In the present work, the identification, sequence analysis, and antioxidant activity of bioaccessible peptides from α-lactalbumin alcalase-hydrolysate was assessed. Antioxidant activity (ABTS, ORAC, and HORAC) of α-lactalbumin showed a significant increase (p<0.05) after the enzymatic treatment with alcalase and this capacity increased even more after the simulation of the gastrointestinal digestion process. Peptides contained in the gastrointestinal digest of α-lactalbumin hydrolysate were separated by preparative RP-HPLC (55 fractions), and three peptides were identified by LC-MS/MS analysis from selected fractions: IWCKDDQNPH (MW: 1254.54Da) f(59-68), KFLDDDLTDDIM (MW: 1439.64Da) f(79-90), DKFLDDDLTDDIM (MW: 1554.67Da) f(78-90). Among the chemically synthesized peptides, IWCKDDQNPH showed the highest antioxidant capacity determined by ORAC, ABTS, and HORAC assays (IC50 0.015± 0.002, 0.45± 0.02, and 1.30± 0.05mg/ml, respectively) and this activity may be related to the amino acid sequence. This is the first report where these bioaccessible peptides from α-lactalbumin hydrolysate were identified. The α-lactalbumin hydrolysate could be employed as a functional antioxidant ingredient. PRACTICAL APPLICATION: The present work studied the bioaccessibility of antioxidant peptides from an α-lactalbumin alcalase-hydrolysate by identifying three novel bioaccessible peptides responsible for the antioxidant capacity, providing evidence of the hydrolysate potential as an antioxidant ingredient in the formulations of functional foods and/or food supplements.

Identification of non-ribosomal peptide synthetase in Ganoderma boninense Pat. that was expressed during the interaction with oil palm

Basal stem rot (BSR) of oil palm is a disastrous disease caused by a white-rot fungus Ganoderma boninense Pat. Non-ribosomal peptides (NRPs) synthesized by non-ribosomal peptide synthetases (NRPSs) are a group of secondary metabolites that act as fungal virulent factors during pathogenesis in the host. In this study, we aimed to isolate NRPS gene of G. boninense strain UPMGB001 and investigate the role of this gene during G. boninense-oil palm interaction. The isolated NRPS DNA fragment of 8322 bp was used to predict the putative peptide sequence of different domains and showed similarity with G. sinense (85%) at conserved motifs of three main NRPS domains. Phylogenetic analysis of NRPS peptide sequences demonstrated that NRPS of G. boninense belongs to the type VI siderophore family. The roots of 6-month-old oil palm seedlings were artificially inoculated for studying NRPS gene expression and disease severity in the greenhouse. The correlation between high disease severity (50%) and high expression (67-fold) of G. boninense NRPS gene at 4 months after inoculation and above indicated that this gene played a significant role in the advancement of BSR disease. Overall, these findings increase our knowledge on the gene structure of NRPS in G. boninense and its involvement in BSR pathogenesis as an effector gene.