Journal articles on the topic 'Peptides – Analysis'
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1
Ito, Toshihiko, Yuki Taguchi, Haruka Oue, Naomi Amano, Yusuke Nagae, Koji Noge, and Katsumi Hashizume. "Formation of taste-active pyroglutamyl peptide ethyl esters in sake by rice koji peptidases." Bioscience, Biotechnology, and Biochemistry 85, no. 6 (March 15, 2021): 1476–84. http://dx.doi.org/10.1093/bbb/zbab041.
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ABSTRACT Formation of taste-active pyroglutamyl (pGlu) peptide ethyl esters in sake was investigated: 2 enzymes (A and B) responsible for the esterification were purified from a rice koji extract. MADLI-TOF/TOF analysis after deglycosylation identified enzyme (A) as peptidase S28 (GenBank accession number OOO13707.1) and enzyme (B) as serine-type carboxypeptidase (accession number AO090010000534). Both enzymes hydrolyzed pGlu peptides and formed ethyl esters under sake mash conditions: acidic pH (3-4) and in ethanol (5%-20% v/v) aqueous solutions. Enzyme (A) formed pGlu penta-peptide ethyl esters from pGlu undeca-peptides by a prolyl endo-type reaction. Enzyme (B) formed (pGlu) deca-peptide and its ethyl esters from pGlu undeca-peptides in an exo-type reaction. We are the first to report the enzymatic ethyl esterification reaction in the formation of pGlu peptides by rice koji peptidases.
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Tani, Naoki, Kohei Kazuma, Yukio Ohtsuka, Yasushi Shigeri, Keiichi Masuko, Katsuhiro Konno, and Hidetoshi Inagaki. "Mass Spectrometry Analysis and Biological Characterization of the Predatory Ant Odontomachus monticola Venom and Venom Sac Components." Toxins 11, no. 1 (January 17, 2019): 50. http://dx.doi.org/10.3390/toxins11010050.
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We previously identified 92 toxin-like peptides and proteins, including pilosulin-like peptides 1–6 from the predatory ant Odontomachus monticola, by transcriptome analysis. Here, to further characterize venom components, we analyzed the venom and venom sac extract by ESI-MS/MS with or without trypsin digestion and reducing agent. As the low-molecular-mass components, we found amino acids (leucine/isoleucine, phenylalanine, and tryptophan) and biogenic amines (histamine and tyramine) in the venom and venom sac extract. As the higher molecular mass components, we found peptides and proteins such as pilosulin-like peptides, phospholipase A2s, hyaluronidase, venom dipeptidyl peptidases, conotoxin-like peptide, and icarapin-like peptide. In addition to pilosulin-like peptides 1–6, we found three novel pilosulin-like peptides that were overlooked by transcriptome analysis. Moreover, pilosulin-like peptides 1–6 were chemically synthesized, and some of them displayed antimicrobial, hemolytic, and histamine-releasing activities.
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Sharmin, K. N., M. A. Amiza, F. Ahmad, S. A. Razali, and F. Hashim. "In silico analysis of Gracilaria changii proteins for potential bioactive peptides." IOP Conference Series: Earth and Environmental Science 967, no. 1 (January 1, 2022): 012017. http://dx.doi.org/10.1088/1755-1315/967/1/012017.
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Abstract Gracilaria changii is a red seaweed species in Malaysia with high protein content (12.57% (dry basis)). Thus, G. changii proteins are potential precursors for producing bioactive peptides. To date, no study has been reported on the potential of G. changii proteins as potential precursors for bioactive peptides. In this study, fourteen G. changii proteins were selected as potential precursors of bioactive peptides using in silico approach. It was found that the most potential bioactivity was dipeptidyl peptidase-IV (DPP IV) inhibitory and angiotensin-I converting enzyme (ACE) inhibitory activities. Papain, ficin and stem bromelain were used for in-silico proteolysis. Stem bromelain was found to be more effective in terms of the release of fragments with a given activity. Furthermore, two tripeptides (ACF and YCL) were screened as novel and promising bioactive peptides. The characteristics of both peptides were also analyzed using PeptideRanker, PepCalc, Peptide Cutter, ToxinPred, AllerTop and AHTpin bioinformatic tools. The bioinformatic tools predicted that both peptides were non-toxic, non-allergen and highly potential. The present work suggests that G. changii can serve as a potential source of bioactive peptides and these findings can provide a basis for future in-vitro and in-vivo study of bioactive peptides from G. changii proteins.
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Zhang, Li, Xuejun Wang, Mengwen Feng, Hao Zhang, Jia Xu, Jingjing Ding, Zijie Cheng, and Lingmei Qian. "Peptidomics Analysis Reveals Peptide PDCryab1 Inhibits Doxorubicin-Induced Cardiotoxicity." Oxidative Medicine and Cellular Longevity 2020 (October 13, 2020): 1–23. http://dx.doi.org/10.1155/2020/7182428.
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Doxorubicin (DOX) is limited due to dose-dependent cardiotoxicity. Peptidomics is an emerging field of proteomics that has attracted much attention because it can be used to study the composition and content of endogenous peptides in various organisms. Endogenous peptides participate in various biological processes and are important sources of candidates for drug development. To explore peptide changes related to DOX-induced cardiotoxicity and to find peptides with cardioprotective function, we compared the expression profiles of peptides in the hearts of DOX-treated and control mice by mass spectrometry. The results showed that 236 differential peptides were identified upon DOX treatment, of which 22 were upregulated and 214 were downregulated. Next, we predicted that 31 peptides may have cardioprotective function by conducting bioinformatics analysis on the domains of each precursor protein, the predicted score of peptide biological activity, and the correlation of each peptide with cardiac events. Finally, we verified that a peptide (SPFYLRPPSF) from Cryab can inhibit cardiomyocyte apoptosis, reduce the production of reactive oxygen species, improve cardiac function, and ameliorate myocardial fibrosis in vitro and vivo. In conclusion, our results showed that the expression profiles of peptides in cardiac tissue change significantly upon DOX treatment and that these differentially expressed peptides have potential cardioprotective functions. Our study suggests a new direction for the treatment of DOX-induced cardiotoxicity.
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Nong, Nhung Thi Phuong, Christoper Caesar Yudho Sutopo, Wei-Ting Hung, Ping-Hsun Wu, and Jue-Liang Hsu. "The Molecular Docking and Inhibition Kinetics of Angiotensin I-Converting Enzyme Inhibitory Peptides Derived from Soft-Shelled Turtle Yolk." Applied Sciences 12, no. 23 (December 2, 2022): 12340. http://dx.doi.org/10.3390/app122312340.
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The soft-shelled turtle yolk (SSTY) protein hydrolysate contains a potential source of bioactive peptides. Our previous study found that five SSTY peptides (WLQL, LPSW, LPLF, VPGLAL and LVGLPL) showed moderate to high dipeptidyl peptidase IV (DPP-IV) inhibitory activities. This study further investigated their angiotensin-I-converting enzyme (ACE) inhibitory activity. Consequently, WLQL was identified as the most potent ACE inhibitory peptide with a remarkably low IC50 value (16.87 ± 0.54 µM). The Lineweaver–Burk plot analysis was performed for the characterization of the peptide’s inhibition mode and the inhibition kinetics was rationalized using the molecular docking simulation. The result revealed that WLQL would dock into the S1 pockets of ACE, while LPSW interacted with ACE’s secondary binding site. Further evaluation of the peptides’ stability against ACE involved a pre-incubation experiment. After 3 h of pre-incubation with ACE, the four peptides were hydrolyzed into smaller fragments with varying degrees, suggesting that they are substrate-type inhibitors. In contrast, LVGLPL can tolerate hydrolysis by ACE and act as a true inhibitor.
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Uttam, Tanishka. "Computational Analysis Comparison Prediction of Anticancer Peptide (ACP)." International Journal for Research in Applied Science and Engineering Technology 10, no. 6 (June 30, 2022): 3316–19. http://dx.doi.org/10.22214/ijraset.2022.44641.
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Abstract: Anticancer peptides (ACPs) contain short peptides composed of 10–60 amino acids that can inhibit tumors cell proliferation or migration, or suppress the formation of tumors blood vessels, and are less likely to cause drug resistance. The aforementioned merits make ACPs the most promising anti-cancer candidate. ACPs may be degraded by proteases and result in cytotoxicity in many cases. To overcome these drawbacks, a plethora of research has focused on the reconstruction or modification of ACPs to improve their anti-cancer activity, while reducing their cytotoxicity. ACPs modification mainly includes main chain reconstruction and side-chain modification. After summarizing the classification and mechanism of action of ACPs, this paper focuses on recent development and progress in their reconstruction and modification. The information collected here may provide some ideas for further research on ACPs, in particular their modification. ACPs were extracted from various search engines like PubMed, Google scholar and Patent lens. Specific searches were carried out using a combination of keywords like ‘ACPs’, ‘antitumor peptides’, ‘anti-angiogenic peptides’, ‘anti-metastatic peptides’ and ‘host defence peptides. The comprehensive information related to a peptide like its source of origin, nature of the peptide, anticancer activity, N- and Cterminal modifications, conformation, etc. Additionally, CancerPPD provides information on around 249 types of cancer cell lines and 16 different assays used for testing the ACPs. In natural peptides, CancerPPD contains peptides having non-natural, chemically modified residues and D-amino acids. Besides this primary information, CancerPPD stores predicted tertiary structures as well as peptide sequences in SMILES format.
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Kawada, Tsuyoshi, Michio Ogasawara, Toshio Sekiguchi, Masato Aoyama, Kohji Hotta, Kotaro Oka, and Honoo Satake. "Peptidomic Analysis of the Central Nervous System of the Protochordate, Ciona intestinalis: Homologs and Prototypes of Vertebrate Peptides and Novel Peptides." Endocrinology 152, no. 6 (April 5, 2011): 2416–27. http://dx.doi.org/10.1210/en.2010-1348.
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The phylogenetic position of ascidians as the chordate invertebrates closest to vertebrates suggests that they might possess homologs and/or prototypes of vertebrate peptide hormones and neuropeptides as well as ascidian-specific peptides. However, only a small number of peptides have so far been identified in ascidians. In the present study, we have identified various peptides in the ascidian, Ciona intestinalis. Mass spectrometry-based peptidomic analysis detected 33 peptides, including 26 novel peptides, from C. intestinalis. The ascidian peptides are largely classified into three categories: 1) prototypes and homologs of vertebrate peptides, such as galanin/galanin-like peptide, which have never been identified in any invertebrates; 2) peptides partially homologous with vertebrate peptides, including novel neurotesin-like peptides; 3) novel peptides. These results not only provide evidence that C. intestinalis possesses various homologs and prototypes of vertebrate neuropeptides and peptide hormones but also suggest that several of these peptides might have diverged in the ascidian-specific evolutionary lineage. All Ciona peptide genes were expressed in the neural complex, whereas several peptide gene transcripts were also distributed in peripheral tissues, including the ovary. Furthermore, a Ciona neurotensin-like peptide, C. intestinalis neurotensin-like peptide 6, was shown to down-regulate growth of Ciona vitellogenic oocytes. These results suggest that the Ciona peptides act not only as neuropeptides in the neural tissue but also as hormones in nonneuronal tissues and that ascidians, unlike other invertebrates, such as nematodes, insects, and sea urchins, established an evolutionary origin of the peptidergic neuroendocrine, endocrine, and nervous systems of vertebrates with certain specific molecular diversity.
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Gaseitsiwe, Simani, Davide Valentini, Raija Ahmed, Shahnaz Mahdavifar, Isabelle Magalhaes, Johannes Zerweck, Mike Schutkowski, et al. "Major Histocompatibility Complex Class II Molecule-Human Immunodeficiency Virus Peptide Analysis Using a Microarray Chip." Clinical and Vaccine Immunology 16, no. 4 (February 18, 2009): 567–73. http://dx.doi.org/10.1128/cvi.00441-08.
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ABSTRACT Identification of major histocompatibility complex (MHC) class II binding peptides is a crucial step in rational vaccine design and immune monitoring. We designed a novel MHC class II molecule-peptide microarray binding assay and evaluated 346 peptides from already identified human immunodeficiency virus (HIV) epitopes and an additional set (n = 206) of 20-mer peptides, overlapping by 15 amino acid residues, from HIV type 1B (HIV-1B) gp160 and Nef as a paradigm. Peptides were attached via the N-terminal part to a linker that covalently binds to the epoxy glass slide. The 552 peptides were printed in triplicate on a single peptide microarray chip and tested for stable formation of MHC class II molecule-peptide complexes using recombinant soluble DRB1*0101(DR1), DRB1*1501(DR2), and DRB1*0401(DR4) molecules. Cluster analysis revealed unique patterns of peptide binding to all three, two, or a single MHC class II molecule. MHC class II binding peptides reside within previously described immunogenic regions of HIV gp160 and Nef, yet we could also identify new MHC class II binding peptides from gp160 and Nef. Peptide microarray chips allow the comprehensive and simultaneous screening of a high number of candidate peptide epitopes for MHC class II binding, guided by subsequent quality data extraction and binding pattern cluster analysis.
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Syvitski, Raymond T., Xiao-Lin Tian, Kamal Sampara, Alan Salman, Song F. Lee, David L. Jakeman, and Yung-Hua Li. "Structure-Activity Analysis of Quorum-Sensing Signaling Peptides from Streptococcus mutans." Journal of Bacteriology 189, no. 4 (August 25, 2006): 1441–50. http://dx.doi.org/10.1128/jb.00832-06.
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ABSTRACT Streptococcus mutans secretes and utilizes a 21-amino-acid signaling peptide pheromone to initiate quorum sensing for genetic competence, biofilm formation, stress responses, and bacteriocin production. In this study, we designed and synthesized a series of truncated peptides and peptides with amino acid substitutions to investigate their structure-activity relationships based on the three-dimensional structures of S. mutans wild-type signaling peptide UA159sp and C-terminally truncated peptide TPC3 from mutant JH1005 defective in genetic competence. By analyzing these peptides, we demonstrated that the signaling peptide of S. mutans has at least two functional domains. The C-terminal structural motif consisting of a sequence of polar hydrophobic charged residues is crucial for activation of the signal transduction pathway, while the core α-helical structure extending from residue 5 to the end of the peptide is required for receptor binding. Peptides in which three or more residues were deleted from the C terminus did not induce genetic competence but competitively inhibited quorum sensing activated by UA159sp. Disruption of the amphipathic α-helix by replacing the Phe-7, Phe-11, or Phe-15 residue with a hydrophilic residue resulted in a significant reduction in or complete loss of the activity of the peptide. In contrast to the C-terminally truncated peptides, these peptides with amino acid substitutions did not compete with UA159sp to activate quorum sensing, suggesting that disruption of the hydrophobic face of the α-helical structure results in a peptide that is not able to bind to the receptor. This study is the first study to recognize the importance of the signaling peptide C-terminal residues in streptococcal quorum sensing.
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Hayes, Maria, Leticia Mora, and Simona Lucakova. "Identification of Bioactive Peptides from Nannochloropsis oculata Using a Combination of Enzymatic Treatment, in Silico Analysis and Chemical Synthesis." Biomolecules 12, no. 12 (December 2, 2022): 1806. http://dx.doi.org/10.3390/biom12121806.
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In vitro ACE-1 inhibitory peptides were characterised previously from a number of microalgal species including Spirulina platensis (peptide IAPG), Chlorella vulgaris (peptides FDL, AFL, VVPPA), Isochrysis galbana (peptide YMGLDLK), Chlorella sorokiniana (peptides IW and LW) and indeed Nannochloropsis oculata (peptides GMNNLTP and LEQ). The isolation of protein from Nannochloropsis oculata using a combination of ammonium salt precipitation and xylanase treatment of resulting biomass combined with molecular weight cut off filtration to produce a permeate and characterisation of bioactive peptides is described. The Angiotensin-1-converting enzyme (ACE-1) IC50 value for the generated permeate fraction was 370 µg/mL. Ninety-five peptide sequences within the permeate fraction were determined using mass spectrometry and eight peptides were selected for chemical synthesis based on in silico analysis. Synthesized peptides were novel based on a search of the literature and relevant databases. In silico, simulated gastrointestinal digestion identified further peptides with bioactivities including ACE-1 inhibitory peptides and peptides with antithrombotic and calcium/calmodulin-dependent kinase II (CAMKII) inhibition. This work highlights the potential of Nannochloropsis oculata biomass as both a protein and bioactive peptide resource, which could be harnessed for use in the development of functional foods and feeds.
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Bracci, Laura, David F. Stroncek, Stefanie Slezak, Giulio C. Spagnoli, and Maurizio Provenzano. "Comprehensive Analysis of CD8 T Cell Immune Response Specific for Two Novel HLA-A*0201 Restriced CMV pp65 Peptides." Blood 106, no. 11 (November 16, 2005): 3928. http://dx.doi.org/10.1182/blood.v106.11.3928.3928.
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Abstract In immune compromised subjects such as patients undergoing bone marrow, organ transplantation or immunosuppressive therapies, Cytomegalovirus (CMV) infection is associated with significant morbidity until the individual’s immune system is completely reconstituted. One method of preventing CMV infection during immune suppression in transplant patients is represented by adoptive administration of CMV peptide-specific cytotoxic T lymphocytes (CTLs) from HLA-matched donors. Despite the strong immunogenicity demonstrated by specific HLA class I peptides, the peptide’s responsiveness varies among individuals. Therefore, it is important to identify additional epitopes for each HLA determinant of interest. In this study we report a comprehensive analysis of CD8 T cell-specific activity against two novel CMV pp65 HLA-A*0201 associated peptides in CMV-experienced HLA-A*0201 subjects. PBMCs from CMV seropositive HLA-A*0201 restricted healthy subjects were peptide-stimulated ex vivo and IFN-γ gene expression was analyzed by qrt-PCR. An IFN-γ ELISPOT assay was carried out on peptide-specific elicited CD8 T lymphocytes to confirm the qrt-PCR results. Tetrameric HLA/epitope complexes (tHLA) were used to track the levels of peptide-specific CD8 T cells responsiveness to cognate epitopes. In addition, in vitro peptide-specific expanded populations of CTLs were used in 51Cr release assay. Based on qrt-PCR results, four out of eight HLA-A*0201 peptides identified by computer algorithms were selected. Two are preaviously published peptides: pp65495–503 (NLVPMVATV) and pp65347–355 (ALFFFDIDL), while two are novel: pp65340–348 (RQYDPVAAL) and pp65310–318 (LMNGQQIFL). In spite the four peptides induced comparable mRNA IFN-γ transcript production, peptides pp65495–503, pp65340–348 and pp65310–318 induced a consistent and sustained IFN-γ protein release and specific killing, while the pp65347–355 failed to induce IFN-γ protein secretion and killing activity (if we exclude a positive IFN-γ protein release after 2-week in vitro induction in one of the donors tested). Comparative assays carried on the functional activity of the three peptides pp65495–503, pp65340–348 and pp65310–318 revealed no intrinsic differences in term of IFN-γ protein release and cytotoxic activity save for the CTL affinity to the HLA-A*0201/epitope complexes (pp65495–503 ~2.6% in nearly 100% of donors vs pp65340–348 ~0.67% or pp65310–318 ~0.77% in nearly one third of the donors after 2-week in vitro induction). The tHLA binding results could be possibly ascribed to differencies in the peptide avidity and stability for the HLA class I. Taken together, these results lead to the conclusion that different peptides can induce a variable levels of immune responses ranging between mere cytokine gene expression and effective cytotoxic activity. In addition, the two novel peptides selected here broaden the panel of potential reagents useful for adoptive immune therapy. Thus, in anticipation of a specific epitope-targeted immune intervention, the three HLA-A*0201 peptides described could be used in combination for adoptive transfer of epitope-specific T cells or epitope-specific vaccination.
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Lichti, Cheryl, Anthony N. Vomund, Orion J. Peterson, Xiaoxiao Wan, and Emil R. Unanue. "Analysis of the nonobese diabetic mouse islet MHC-II peptidome reveals posttranslationally modified autoantigens." Journal of Immunology 204, no. 1_Supplement (May 1, 2020): 142.12. http://dx.doi.org/10.4049/jimmunol.204.supp.142.12.
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Abstract Autoimmune diabetes results from the destruction of insulin-producing beta cells, a process initiated by CD4 T cells recognizing MHC-II bound beta cell-derived peptides. We identified MHC-II bound peptides in the islets and throughout the peripheral lymphatic system in order to better understand diabetes initiation and progression. Toward this end, we performed unbiased nanoflow liquid chromatography-tandem mass spectrometry (nLC-MS/MS) analysis to obtain sequence information for MHC-II peptides isolated from islets, pancreatic lymph nodes and spleens of nonobese diabetic (NOD) mice. Peptides derived from beta cell proteins were further examined for their relative I-Ag7 binding strength and CD4 T cell autoreactivity. For a discussion of the major immunogenic peptides derived from the B chain of insulin and from C peptide, see the abstract of Wan et al. Herein we discuss the finding of a deamidated C peptide fragment and our search for fused peptides. We identified the deamidated insulin-1 C peptide fragment Ins1C:51–61, LQTLALEVARE. Evidence in the literature supports this C-terminal deamidation as being spontaneous rather than enzyme-mediated. Deamidation improved I-Ag7 binding compared to the wild type peptide and increased its immunogenicity, demonstrating the biological importance of this modification. The homologous peptide from insulin-2 was not identified, indicating a possible sequence bias for spontaneous deamidation. We identified only one fused peptide bound to I-Ag7, an insulin C peptide-islet amyloid polypeptide hybrid insulin peptide (HIP) that matches the previously reported HIP6.9. We also identified several free fused peptides in crinosomes and posit this as the probable site of their formation.
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Yates, John R., Edwin Carmack, Lara Hays, and Jimmy Eng. "High Throughput Analysis of Tandem Mass Spectrometry Data for Peptides." Laboratory Automation News 2, no. 2 (May 1997): 28–31. http://dx.doi.org/10.1177/221106829700200206.
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In recent years tandem mass spectrometry has made a substantial impact on the sequence analysis of peptides ( 1 ). In this process peptide ions are dissociated in a collision cell to produce a collection of fragment ions. The m/z values of the fragment ions are determined in the second mass analyzer. Fortuitously, peptide ions fragment primarily around the amide linkages or peptide bonds in a manner that produces a ladder of sequence ions. This method of analysis for peptides has several advantages; high throughput and sensitivity, the ability to analyze peptides contained in mixtures, and lastly the ability to observe covalent modifications to the structure.
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Kraszewska, Joanna, Michael C. Beckett, Tharappel C. James, and Ursula Bond. "Comparative Analysis of the Antimicrobial Activities of Plant Defensin-Like and Ultrashort Peptides against Food-Spoiling Bacteria." Applied and Environmental Microbiology 82, no. 14 (May 6, 2016): 4288–98. http://dx.doi.org/10.1128/aem.00558-16.
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ABSTRACTAntimicrobial peptides offer potential as novel therapeutics to combat food spoilage and poisoning caused by pathogenic and nonpathogenic bacteria. Our previous studies identified the peptide human beta-defensin 3 (HBD3) as a potent antimicrobial agent against a wide range of beer-spoiling bacteria. Thus, HBD3 is an excellent candidate for development as an additive to prevent food and beverage spoilage. To expand the repertoire of peptides with antimicrobial activity against bacteria associated with food spoilage and/or food poisoning, we carried out anin silicodiscovery pipeline to identify peptides with structure and activity similar to those of HBD3, focusing on peptides of plant origin. Using a standardized assay, we compared the antimicrobial activities of nine defensin-like plant peptides to the activity of HBD3. Only two of the peptides, fabatin-2 and Cp-thionin-2, displayed antimicrobial activity; however, the peptides differed from HBD3 in being sensitive to salt and were thermostable. We also compared the activities of several ultrashort peptides to that of HBD3. One of the peptides, the synthetic tetrapeptide O3TR, displayed biphasic antimicrobial activity but had a narrower host range than HBD3. Finally, to determine if the peptides might act in concert to improve antimicrobial activity, we compared the activities of the peptides in pairwise combinations. The plant defensin-like peptides fabatin-2 and Cp-thionin-2 displayed a synergistic effect with HBD3, while O3TR was antagonistic. Thus, some plant defensin-like peptides are effective antimicrobials and may act in concert with HBD3 to control bacteria associated with food spoilage and food poisoning.IMPORTANCEFood spoilage and food poisoning caused by bacteria can have major health and economic implications for human society. With the rise in resistance to conventional antibiotics, there is a need to identify new antimicrobials to combat these outbreaks in our food supply. Here we screened plant peptide databases to identify peptides that share structural similarity with the human defensin peptide HBD3, which has known antimicrobial activity against food-spoiling bacteria. We show that two of the plant peptides display antimicrobial activity against bacteria associated with food spoilage. When combined with HBD3, the peptides are highly effective. We also analyzed the activity of an easily made ultrashort synthetic peptide, O3TR. We show that this small peptide also displays antimicrobial activity against food-spoiling bacteria but is not as effective as HBD3 or the plant peptides. The plant peptides identified are good candidates for development as natural additives to prevent food spoilage.
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Burkitt, William I., Anastassios E. Giannakopulos, Foteini Sideridou, Sajid Bashir, and Peter J. Derrick. "Discrimination Effects in MALDI-MS of Mixtures of Peptides—Analysis of the Proteome." Australian Journal of Chemistry 56, no. 5 (2003): 369. http://dx.doi.org/10.1071/ch02155.
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Peptide ion suppression in matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) can hinder the detection of site-specific post-translational protein modifications. Within a peptide mixture, the presence or absence of a particular peptide can affect the ion intensities of other peptides in the mixture. These effects have been studied using equimolar solutions of target peptides and observation of the increase or decrease in ion intensity of the peptides upon the removal or addition of individual peptides. Gas-phase basicities and hydrophobicity measures have been used to rationalize this behaviour. ZipTips have been used to remove impurities and reduce the number of peptides present at any moment in a solution, a procedure that results in a significant increase in the total percentage of the amino acid coverage of enzymatically digested proteins. The efficacy of this approach was demonstrated using specifically nitrated lysozyme and specifically nitrated myoglobin.
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Momburg, F., J. Roelse, G. J. Hämmerling, and J. J. Neefjes. "Peptide size selection by the major histocompatibility complex-encoded peptide transporter." Journal of Experimental Medicine 179, no. 5 (May 1, 1994): 1613–23. http://dx.doi.org/10.1084/jem.179.5.1613.
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The major histocompatibility complex (MHC)-encoded heterodimeric TAP1/TAP2 transporter (TAP) translocates cytosolic peptides into the lumen of the endoplasmic reticulum (ER), where peptides of 8 to 11 amino acids long associate with MHC class I molecules. We have studied the selectivity of peptide translocation by TAP in streptolysin O-permeabilized cells using glycosylatable, radioiodinated model peptides to detect import into the ER lumen. TAP-dependent translocation of a radiolabeled nonamer peptide was most efficiently inhibited by unlabeled 9- to 11-mer peptides. Peptides between 7 and 40 amino acids long all could inhibit transport, the longer peptides being least effective. Also, peptides shorter than eight amino acids were inefficiently translocated. The use of directly labeled length variants in translocation assays and TLC analysis of the transported material revealed two pathways for translocation: short peptides (7 to 13 amino acids long) were translocated without prior modification. In contrast, transport of longer peptides was not effective. Instead such peptides were clipped by cytosolic peptidases before efficient transport. Our data suggest that TAP preferentially translocates peptides of appropriate length for class I binding. Furthermore, TAP-translocated peptides were rapidly released from the ER unless they were trapped there by being glycosylated or by binding to MHC class I molecules.
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Liu, Xiaoguang, Xia Ning, Yan Zhang, Wenfeng Chen, Zhangwu Zhao, and Qingwen Zhang. "Peptidomic Analysis of the Brain and Corpora Cardiaca-Corpora Allata Complex in the Bombyx mori." International Journal of Peptides 2012 (December 17, 2012): 1–11. http://dx.doi.org/10.1155/2012/640359.
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The silkworm, Bombyx mori, is an important economic insect for silk production. However, many of the mature peptides relevant to its various life stages remain unknown. Using RP-HPLC, MALDI-TOF MS, and previously identified peptides from B. mori and other insects in the transcriptome database, we created peptide profiles showing a total of 6 ion masses that could be assigned to peptides in eggs, including one previously unidentified peptide. A further 49 peptides were assigned to larval brains. 17 new mature peptides were identified in isolated masses. 39 peptides were found in pupal brains with 8 unidentified peptides. 48 were found in adult brains with 12 unidentified peptides. These new unidentified peptides showed highly significant matches in all MS analysis. These matches were then searched against the National Center for Biotechnology Information (NCBI) database to provide new annotations for these mature peptides. In total, 59 mature peptides in 19 categories were found in the brains of silkworms at the larval, pupal, and adult stages. These results demonstrate that peptidomic variation across different developmental stages can be dramatic. Moreover, the corpora cardiaca-corpora allata (CC-CA) complex was examined during the fifth larval instar. A total of 41 ion masses were assigned to peptides.
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Skerlavaj, Barbara, Marco Scocchi, Renato Gennaro, Angela Risso, and Margherita Zanetti. "Structural and Functional Analysis of Horse Cathelicidin Peptides." Antimicrobial Agents and Chemotherapy 45, no. 3 (March 1, 2001): 715–22. http://dx.doi.org/10.1128/aac.45.3.715-722.2001.
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ABSTRACT Cathelicidin-derived antimicrobial peptides are a component of the peptide-based host defense of neutrophils and epithelia, with a widespread distribution in mammals. We recently reported the cDNA sequences of three putative horse myeloid cathelicidins, named eCATH-1, -2, and -3. A Western analysis was performed to investigate their presence in neutrophils and processing to mature peptides. eCATH-2 and eCATH-3, but not eCATH-1, were found to be present in uncleaved forms in horse neutrophils. The corresponding mature peptides were detected in inflammatory sites, suggesting that processing of the propeptides takes place upon neutrophil activation. A functional characterization was then performed with synthetic eCATH peptides. Circular dichroism measurements indicated an amphipathic α-helical conformation of these peptides in an anisotropic environment, and in vitro assays revealed a potent activity and a broad spectrum of antimicrobial activity for eCATH-1 and a somewhat more restricted spectrum of activity for eCATH-2. Conversely, a strong dependence on salt concentration was observed when the activity of eCATH-3 was tested. This peptide efficiently killed bacteria and some fungal species, i.e.,Cryptococcus neoformans and Rhodotorula rubra, in low-ionic-strength media, but the activity was inhibited in the presence of physiological salt medium. This behavior could be modified by modulating the amphipathicity of the molecule. In fact, the synthetic analogue LLK-eCATH-3, with a slightly modified sequence that increases the hydrophobic moment of the peptide, displayed a potent activity in physiological salt medium against the strains resistant to eCATH-3 under these conditions.
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Delgado, Julio, Hernando Escobar, David Crockett, Eduardo Reyes-Vargas, and Peter Jensen. "Analysis of the performance of peptide predicting methods using MHC class I peptide sequencing in the C57BL/6 mouse (78.11)." Journal of Immunology 182, no. 1_Supplement (April 1, 2009): 78.11. http://dx.doi.org/10.4049/jimmunol.182.supp.78.11.
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Abstract MHC class I peptide-binding motifs can defined by sequencing of peptides naturally bound to MHC class I molecules. More recently MHC class I-peptide binding motifs have be defined on the basis of quantitative MHC-peptide binding assays in vitro using peptide libraries. The information on peptide binding motifs obtained using binding assays have been useful to develop numerous bioinformatics-based tools to predict the binding of peptides to MHC class I molecules. To date few studies have analyzed the performance of these bioinformatics tools to predict peptides determined by sequencing of peptides eluted directly from MHC class I molecules. In this study we performed sequencing of endogenous peptides eluted from H2Kb and Db molecules expressed in the C57BL/6 mouse. Using data from 280 H2-class I-bound peptides we identified novel preferred anchor residues located in H2Kb and H2Db-associated peptides. When comparing the predicting affinity performance of 3 bioinformatics tools we found that between 60 to 95% of peptides eluted from H2Kb and H2Db molecules were correctly classified as binders by these 3 predicting algorithms, suggesting that these bioinformatics tools are reliable and efficient for prediction of naturally processed MHC class I ligands. These results expand our knowledge about H2 class I binding specificities and provide the identity of positions that can be used for better characterization of H2 class I peptide-binding motifs. Similar studies using sensitive methods for sequencing large numbers of peptides from other MHC molecules are needed to establish more precise motif information that can be used for the training of bioinformatics tool employed in the prediction of CD8 T-cell epitopes
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Neagu, Anca-Narcisa, Madhuri Jayathirtha, Emma Baxter, Mary Donnelly, Brindusa Alina Petre, and Costel C. Darie. "Applications of Tandem Mass Spectrometry (MS/MS) in Protein Analysis for Biomedical Research." Molecules 27, no. 8 (April 8, 2022): 2411. http://dx.doi.org/10.3390/molecules27082411.
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Mass Spectrometry (MS) allows the analysis of proteins and peptides through a variety of methods, such as Electrospray Ionization-Mass Spectrometry (ESI-MS) or Matrix-Assisted Laser Desorption Ionization-Mass Spectrometry (MALDI-MS). These methods allow identification of the mass of a protein or a peptide as intact molecules or the identification of a protein through peptide-mass fingerprinting generated upon enzymatic digestion. Tandem mass spectrometry (MS/MS) allows the fragmentation of proteins and peptides to determine the amino acid sequence of proteins (top-down and middle-down proteomics) and peptides (bottom-up proteomics). Furthermore, tandem mass spectrometry also allows the identification of post-translational modifications (PTMs) of proteins and peptides. Here, we discuss the application of MS/MS in biomedical research, indicating specific examples for the identification of proteins or peptides and their PTMs as relevant biomarkers for diagnostic and therapy.
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Kowalska, Marta, Dominik Popiel, Martyna Walter, Remigiusz Bąchor, Monika Biernat, Marek Cebrat, Monika Kijewska, Mariola Kuczer, Maciej Modzel, and Alicja Kluczyk. "Veni, Vidi, Vici: Immobilized Peptide-Based Conjugates as Tools for Capture, Analysis, and Transformation." Chemosensors 10, no. 1 (January 12, 2022): 31. http://dx.doi.org/10.3390/chemosensors10010031.
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Analysis of peptide biomarkers of pathological states of the organism is often a serious challenge, due to a very complex composition of the cell and insufficient sensitivity of the current analytical methods (including mass spectrometry). One of the possible ways to overcome this problem is sample enrichment by capturing the selected components using a specific solid support. Another option is increasing the detectability of the desired compound by its selective tagging. Appropriately modified and immobilized peptides can be used for these purposes. In addition, they find application in studying the specificity and activity of proteolytic enzymes. Immobilized heterocyclic peptide conjugates may serve as metal ligands, to form complexes used as catalysts or analytical markers. In this review, we describe various applications of immobilized peptides, including selective capturing of cysteine-containing peptides, tagging of the carbonyl compounds to increase the sensitivity of their detection, enrichment of biological samples in deoxyfructosylated peptides, and fishing out of tyrosine–containing peptides by the formation of azo bond. Moreover, the use of the one-bead-one-compound peptide library for the analysis of substrate specificity and activity of caspases is described. Furthermore, the evolution of immobilization from the solid support used in peptide synthesis to nanocarriers is presented. Taken together, the examples presented here demonstrate immobilized peptides as a multifunctional tool, which can be successfully used to solve multiple analytical problems.
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Wang, Guangshun. "Bioinformatic Analysis of 1000 Amphibian Antimicrobial Peptides Uncovers Multiple Length-Dependent Correlations for Peptide Design and Prediction." Antibiotics 9, no. 8 (August 7, 2020): 491. http://dx.doi.org/10.3390/antibiotics9080491.
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Amphibians are widely distributed on different continents, except for the polar regions. They are important sources for the isolation, purification and characterization of natural compounds, including peptides with various functions. Innate immune antimicrobial peptides (AMPs) play a critical role in warding off invading pathogens, such as bacteria, fungi, parasites, and viruses. They may also have other biological functions such as endotoxin neutralization, chemotaxis, anti-inflammation, and wound healing. This article documents a bioinformatic analysis of over 1000 amphibian antimicrobial peptides registered in the Antimicrobial Peptide Database (APD) in the past 18 years. These anuran peptides were discovered in Africa, Asia, Australia, Europe, and America from 1985 to 2019. Genomic and peptidomic studies accelerated the discovery pace and underscored the necessity in establishing criteria for peptide entry into the APD. A total of 99.9% of the anuran antimicrobial peptides are less than 50 amino acids with an average length of 24 and a net charge of +2.5. Interestingly, the various amphibian peptide families (e.g., temporins, brevinins, esculentins) can be connected through multiple length-dependent relationships. With an increase in length, peptide net charge increases, while the hydrophobic content decreases. In addition, glycine, leucine, lysine, and proline all show linear correlations with peptide length. These correlations improve our understanding of amphibian peptides and may be useful for prediction and design of new linear peptides with potential applications in treating infectious diseases, cancer and diabetes.
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Chandra, Deepika, P. Gayathri, Mudita Vats, R. Nagaraj, MK Ray, and MV Jagannadham. "Mass spectral analysis of acetylated peptides: Implications in proteomics." European Journal of Mass Spectrometry 26, no. 1 (June 24, 2019): 36–45. http://dx.doi.org/10.1177/1469066719857564.
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Sequence determination of peptides using mass spectrometry plays a crucial role in the bottom-up approaches for the identification of proteins. It is crucially important to minimise false detection and validate sequence of the peptides in order to correctly identify a protein. Chemical modification of peptides followed by mass spectrometry is an option for improving the spectral quality. In silico-derived tryptic peptides with different N-terminal amino acids were designed from human proteins and synthesized. The effect of acetylation on the fragmentation of peptides was studied. N-terminal acetylation of the tryptic peptides was shown to form b1-ions, improve the abundance and occurrence of b-ions. In some cases, the intensity and occurrence of some y-ions also varied. Thus, it is demonstrated that acetylation plays an important role in improving the de novo sequencing efficiency of the peptides. The acetylation method was extended to tryptic peptides generated from the proteome of an Antarctic bacterium Pseudomonas syringae Lz4W using the proteomics work flow and mass spectra of the peptides were analysed. Comparison of the MS/MS spectra of the acetylated and unacetylated peptides revealed that acetylation helped in improving the spectral quality and validated the peptide sequences. Using this method, 673 proteins of the 1070 proteins identified were validated.
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Larive, Cynthia K., Dimuthu Jayawickrama, and Laszlo Orfi. "Quantitative Analysis of Peptides with NMR Spectroscopy." Applied Spectroscopy 51, no. 10 (October 1997): 1531–36. http://dx.doi.org/10.1366/0003702971939055.
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The determination of peptide concentration with 1H nuclear magnetic resonance (NMR) spectroscopy using an internal standard or an external standard in a sealed glass capillary was investigated for three tyrosine-containing tripeptides. Trimethylsilylpropionic acid (TSP) and maleic acid were tested as external standards for quantitation by proton NMR. Although comparable results were obtained for either standard, the performance of maleic acid was found to be superior because of its better long-term stability in the sealed capillary. Loss of TSP from solution occurred over time due to adsorption onto the walls of the capillary, necessitating frequent recalibration against the primary standard, potassium acid phthalate (KHP). The peptide contents of solid peptides determined with 1H NMR are compared with those obtained from ultraviolet (UV) absorbance measurements of the tyrosine chromophore. The versatility of NMR for the quantitative analysis of peptides that do not contain an appropriate UV chromophore make it well-suited for the determination of peptide concentration in aggregation studies or for the preparation of solutions for high-throughput screening of biological activity.
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Paziewska, Agnieszka, Marcin Polkowski, Tymon Rubel, Jakub Karczmarski, Anna Wiechowska-Kozlowska, Michalina Dabrowska, Michal Mikula, Michal Dadlez, and Jerzy Ostrowski. "Mass Spectrometry-Based Comprehensive Analysis of Pancreatic Cyst Fluids." BioMed Research International 2018 (November 29, 2018): 1–12. http://dx.doi.org/10.1155/2018/7169595.
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Pancreatic cyst fluids (PCFs) enriched in tumour-derived proteins are considered a potential source of new biomarkers. This study aimed to determine compositional and quantitative differences between the degradome and proteome of PCFs aspirated from different types of pancreatic cyst lesions (PCLs). 91 patients who underwent endoscopic ultrasound-fine needle aspiration under routine clinical diagnosis of PCLs were enrolled. Four cysts were malignant (CAs), and 87 were nonmalignant and consisted of 18 intraductal papillary mucinous neoplasms (IPMNs), 14 mucinous cystic neoplasms (MCNs), nine serous cystic neoplasms (SCNs), 29 pseudocysts (PCs), and 17 unclassified. Profiles of the <5 kDa fraction, the degradome, and the trypsin-digested proteome were analysed using an LTQ-Orbitrap Elite mass spectrometer coupled with a nanoACQUITY LC system. Qualitative analyses identified 796 and 366 proteins in degradome and proteome, respectively, and 689 (77%) and 285 (78%) of them were present in the Plasma Proteome Database. Gene Ontology analysis showed a significant overrepresentation of peptidases and peptidases inhibitors in both datasets. In the degradome fraction, quantitative values were obtained for 6996 peptides originating from 657 proteins. Of these, 2287 peptides were unique to a single type, and 515 peptides, derived from 126 proteins, were shared across cyst types. 32 peptides originating from 12 proteins had differential (adjustedp-value ≤0.05, FC ≥1.5) abundance in at least one of the five cysts types. In proteome, relative expression was measured for 330 proteins. Of them, 33 proteins had significantly (adjustedp-value ≤0.05, FC ≥1.5) altered abundance in at least one of the studied groups and 19 proteins appeared to be unique to a given cyst type. PCFs are dominated by blood proteins and proteolytic enzymes. Although differences in PCF peptide composition and abundance could aid classification of PCLs, the unpredictable inherent PCF proteolytic activity may limit the practical applications of PCF protein profiling.
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Ma, Menglin, Jihong Li, and Bruce A. McClane. "Structure-Function Analysis of Peptide Signaling in the Clostridium perfringens Agr-Like Quorum Sensing System." Journal of Bacteriology 197, no. 10 (March 16, 2015): 1807–18. http://dx.doi.org/10.1128/jb.02614-14.
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ABSTRACTThe accessory growth regulator (Agr)-like quorum sensing (QS) system ofClostridium perfringenscontrols the production of many toxins, including beta toxin (CPB). We previously showed (J. E. Vidal, M. Ma, J. Saputo, J. Garcia, F. A. Uzal, and B. A. McClane, Mol Microbiol 83:179–194, 2012,http://dx.doi.org/10.1111/j.1365-2958.2011.07925.x) that an 8-amino-acid, AgrD-derived peptide named 8-R upregulates CPB production by this QS system. The current study synthesized a series of small signaling peptides corresponding to sequences within theC. perfringensAgrD polypeptide to investigate theC. perfringensautoinducing peptide (AIP) structure-function relationship. When both linear and cyclic ring forms of these peptides were added toagrBnull mutants of type B strain CN1795 or type C strain CN3685, the 5-amino-acid peptides, whether in a linear or ring (thiolactone or lactone) form, induced better signaling (more CPB production) than peptide 8-R for bothC. perfringensstrains. The 5-mer thiolactone ring peptide induced faster signaling than the 5-mer linear peptide. Strain-related variations in sensing these peptides were detected, with CN3685 sensing the synthetic peptides more strongly than CN1795. Consistent with those synthetic peptide results, Transwell coculture experiments showed that CN3685 exquisitely senses native AIP signals from other isolates (types A, B, C, and D), while CN1795 barely senses even its own AIP. Finally, aC. perfringensAgrD sequence-based peptide with a 6-amino-acid thiolactone ring interfered with CPB production by severalC. perfringensstrains, suggesting potential therapeutic applications. These results indicate that AIP signaling sensitivity and responsiveness vary amongC. perfringensstrains and suggestC. perfringensprefers a 5-mer AIP to initiate Agr signaling.IMPORTANCEClostridium perfringenspossesses an Agr-like quorum sensing (QS) system that regulates virulence, sporulation, and toxin production. The current study used synthetic peptides to identify the structure-function relationship for the signaling peptide that activates this QS system. We found that a 5-mer peptide induces optimal signaling. Unlike other Agr systems, a linear version of this peptide (in addition to thiolactone and lactone versions) could induce signaling. TwoC. perfringensstrains were found to vary in sensitivity to these peptides. We also found that a 6-mer peptide can inhibit toxin production by some strains, suggesting therapeutic applications.
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Zhou, Zemin, Eduardo Reyes-Vargas, Hernando Escobar, Kuan Chang, Alan Rockwood, Julio Delgado, Xiao He, and Peter Jensen. "Peptidomic analysis of type-1 diabetes associated HLA-DQ molecules and impact of HLA-DM editing (APP5P.108)." Journal of Immunology 194, no. 1_Supplement (May 1, 2015): 183.10. http://dx.doi.org/10.4049/jimmunol.194.supp.183.10.
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Abstract HLA-DM is critical in editing peptide repertoires presented by APC, thus influencing the selection/activation of CD4+ T cells. We previously reported that type-1 diabetes (T1D) associated HLA-DQ2, 8 & DQ2/8 molecules (DQs) are relatively resistant to DM editing of the CLIP peptides. In this study, we further studied DM sensitivity of T1D-associated DQs by peptidomic analysis. Compared to a T1D-protective DQ6, the percentages of shared peptides among T1D-associated DQs were significantly higher. There were greater numbers of nested peptide sets and long peptides (>20 aa) eluted from T1D-associated DQs. Predicted peptide binding motifs of DQ2, 8 & 2/8 shared charged anchor residues, while hydrophobic anchors were present in DQ6 peptides. Competition binding assays comparing the eluted peptides from DM sensitive, dependent, or resistant groups showed that the binding affinities of the DM sensitive peptides were significantly lower than that of CLIP1 peptide. The increased sDQ8-CLIP1 complex stability, with the intrinsic half-life of 58 h measured by fluorescence polarization assay, was 8 times longer than that of sDQ6-CLIP1 (7 h), further supporting the DM resistance of T1D associated DQs. Collectively, T1D associated DQs share distinct characteristics, including binding of peptides from known T1D auto-antigens. Our new data further support the hypothesis that DM resistance in T1D associated DQs affects the peptide repertoires, thus contributing to the pathogenesis of T1D.
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Stephenson, Sophie, Christian Mueller, Min Jiang, and Marta Perego. "Molecular Analysis of Phr Peptide Processing in Bacillus subtilis." Journal of Bacteriology 185, no. 16 (August 15, 2003): 4861–71. http://dx.doi.org/10.1128/jb.185.16.4861-4871.2003.
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ABSTRACT In Bacillus subtilis, an export-import pathway regulates production of the Phr pentapeptide inhibitors of Rap proteins. Processing of the Phr precursor proteins into the active pentapeptide form is a key event in the initiation of sporulation and competence development. The PhrA (ARNQT) and PhrE (SRNVT) peptides inhibit the RapA and RapE phosphatases, respectively, whose activity is directed toward the Spo0F∼P intermediate response regulator of the sporulation phosphorelay. The PhrC (ERGMT) peptide inhibits the RapC protein acting on the ComA response regulator for competence with regard to DNA transformation. The structural organization of PhrA, PhrE, and PhrC suggested a role for type I signal peptidases in the processing of the Phr preinhibitor, encoded by the phr genes, into the proinhibitor form. The proinhibitor was then postulated to be cleaved to the active pentapeptide inhibitor by an additional enzyme. In this report, we provide evidence that Phr preinhibitor proteins are subject to only one processing event at the peptide bond on the amino-terminal end of the pentapeptide. This processing event is most likely independent of type I signal peptidase activity. In vivo and in vitro analyses indicate that none of the five signal peptidases of B. subtilis (SipS, SipT, SipU, SipV, and SipW) are indispensable for Phr processing. However, we show that SipV and SipT have a previously undescribed role in sporulation, competence, and cell growth.
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Pullen, Jeffrey K., George W. Anderson, Susan L. Welkos, and Arthur M. Friedlander. "Analysis of the Yersinia pestis V Protein for the Presence of Linear Antibody Epitopes." Infection and Immunity 66, no. 2 (February 1, 1998): 521–27. http://dx.doi.org/10.1128/iai.66.2.521-527.1998.
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ABSTRACT The V protein expressed by pathogenic Yersinia pestisis an important virulence factor and protective immunogen. The presence of linear B-cell epitopes in the V protein was investigated by using a series of 17 overlapping linear peptides. Groups of 10 mice were immunized intraperitoneally with 30 μg of each peptide on days 0, 30, and 60. Although the V protein-specific antibody response to the peptides varied, most of the peptides elicited high antibody titers. The immunized mice were challenged subcutaneously with 60 50% lethal doses (LD50) (1 LD50 = 1.9 CFU) of a virulent Y. pestis strain, CO92. None of the peptide-immunized mice survived challenge. The animals immunized with the V protein were completely protected against challenge. The immunogenicity of some of the V peptides was increased by conjugating them to keyhole limpet hemocyanin. Only one peptide (encompassing amino acids 1 to 30) conjugate demonstrated some protection; the others were not protective. In additional experiments, V peptides that reacted well with sera from mice surviving Y. pestis infection were combined and used to immunize mice. Although the combined peptides appeared to be very immunogenic, they were not protective. Therefore, the protective B-lymphocyte epitope(s) in the V protein is most likely to be conformational.
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Tussey, L. G., M. Matsui, S. Rowland-Jones, R. Warburton, J. A. Frelinger, and A. McMichael. "Analysis of mutant HLA-A2 molecules. Differential effects on peptide binding and CTL recognition." Journal of Immunology 152, no. 3 (February 1, 1994): 1213–21. http://dx.doi.org/10.4049/jimmunol.152.3.1213.
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Abstract Previous studies have identified several residues lining the groove of the HLA-A2.1 molecule that are critical for Ag presentation. However, it is not clear whether these residues are critical for binding of the peptide epitope per se or for determining the appropriate conformation of bound peptide. To distinguish between these possibilities, mutations at eight of these residues have been tested for their effects on the ability of the molecule to bind and present two known peptide epitopes--one derived from the influenza A matrix protein, the other from HIV pol. With only one exception, the mutations were found to affect the binding of the two peptides similarly. Most of the mutations resulted in intermediate deleterious effects on binding, with the B pocket mutant F9Y having the most dramatic negative effect on binding for both peptides. Two of the mutations significantly enhanced binding of both peptides and a peptide-specific effect on binding was seen with the substitution, Y99H, which enhanced binding of the matrix peptide yet diminished binding of the pol peptide. In contrast to the effects on binding, the effects of the mutations on presentation differed considerably for the two peptides. The most striking difference was seen with two alpha 2 alpha helix mutants that are fully recognized by pol peptide-specific CTL but not recognized by matrix peptide-specific CTL even though levels of binding were comparably diminished for the two peptides. These results suggest that some interactions, although not critical for binding per se, are critical for functional binding and the importance of these interactions differs among peptide epitopes.
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Kraft, Jennifer R., Russell E. Vance, Jan Pohl, Amy M. Martin, David H. Raulet, and Peter E. Jensen. "Analysis of Qa-1bPeptide Binding Specificity and the Capacity of Cd94/Nkg2a to Discriminate between Qa-1–Peptide Complexes." Journal of Experimental Medicine 192, no. 5 (August 28, 2000): 613–24. http://dx.doi.org/10.1084/jem.192.5.613.
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The major histocompatibility complex class Ib protein, Qa-1b, serves as a ligand for murine CD94/NKG2A natural killer (NK) cell inhibitory receptors. The Qa-1b peptide-binding site is predominantly occupied by a single nonameric peptide, Qa-1 determinant modifier (Qdm), derived from the leader sequence of H-2D and L molecules. Five anchor residues were identified in this study by measuring the peptide-binding affinities of substituted Qdm peptides in experiments with purified recombinant Qa-1b. A candidate peptide-binding motif was determined by sequence analysis of peptides eluted from Qa-1 that had been folded in the presence of random peptide libraries or pools of Qdm derivatives randomized at specific anchor positions. The results indicate that Qa-1b can bind a diverse repertoire of peptides but that Qdm has an optimal primary structure for binding Qa-1b. Flow cytometry experiments with Qa-1b tetramers and NK target cell lysis assays demonstrated that CD94/NKG2A discriminates between Qa-1b complexes containing peptides with substitutions at nonanchor positions P4, P5, or P8. Our findings suggest that it may be difficult for viruses to generate decoy peptides that mimic Qdm and raise the possibility that competitive replacement of Qdm with other peptides may provide a novel mechanism for activation of NK cells.
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Sin, Wai-Ching, Hon-Ming Lam, and Sai-Ming Ngai. "Identification of Diverse Stress-Responsive Xylem Sap Peptides in Soybean." International Journal of Molecular Sciences 23, no. 15 (August 3, 2022): 8641. http://dx.doi.org/10.3390/ijms23158641.
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Increasing evidence has revealed that plant secretory peptides are involved in the long-distance signaling pathways that help to regulate plant development and signal stress responses. In this study, we purified small peptides from soybean (Glycine max) xylem sap via o-chlorophenol extraction and conducted an in-depth peptidomic analysis using a mass spectrometry (MS) and bioinformatics approach. We successfully identified 14 post-translationally modified peptide groups belonging to the peptide families CEP (C-terminally encoded peptides), CLE (CLAVATA3/embryo surrounding region-related), PSY (plant peptides containing tyrosine sulfation), and XAP (xylem sap-associated peptides). Quantitative PCR (qPCR) analysis showed unique tissue expression patterns among the peptide-encoding genes. Further qPCR analysis of some of the peptide-encoding genes showed differential stress-response profiles toward various abiotic stress factors. Targeted MS-based quantification of the nitrogen deficiency-responsive peptides, GmXAP6a and GmCEP-XSP1, demonstrated upregulation of peptide translocation in xylem sap under nitrogen-deficiency stress. Quantitative proteomic analysis of GmCEP-XSP1 overexpression in hairy soybean roots revealed that GmCEP-XSP1 significantly impacts stress response-related proteins. This study provides new insights that root-to-shoot peptide signaling plays important roles in regulating plant stress-response mechanisms.
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Helal, Ahmed, Sara Pierri, Davide Tagliazucchi, and Lisa Solieri. "Effect of Fermentation with Streptococcus thermophilus Strains on In Vitro Gastro-Intestinal Digestion of Whey Protein Concentrates." Microorganisms 11, no. 7 (July 3, 2023): 1742. http://dx.doi.org/10.3390/microorganisms11071742.
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Three Streptococcus thermophilus strains, namely RBC6, RBC20, and RBN16, were proven to release bioactive peptides during whey protein concentrate (WPC) fermentation, resulting in WPC hydrolysates with biological activities. However, these bioactive peptides can break down during gastro-intestinal digestion (GID), hindering the health-promoting effect of fermented WPC hydrolysates in vivo. In this work, the effect of simulated GID on three WPC hydrolysates fermented with S. thermophilus strains, as well as on unfermented WPC was studied in terms of protein hydrolysis, biological activities, and peptidomics profiles, respectively. In general, WPC fermentation enhanced protein hydrolysis compared to unfermented WPC. After in vitro GID, WPC fermented with S. thermophilus RBC20 showed the highest antioxidant activity, whereas WPC fermented with strain RBC06 displayed the highest angiotensin-converting enzyme (ACE)- and dipeptidyl peptidase IV (DPP-IV)-inhibitory activities. Peptidomics analysis revealed that all digested WPC samples were highly similar to each other in peptide profiles, and 85% of the 46 identified bioactive peptides were shared among fermented and unfermented samples. However, semi-quantitative analysis linked the observed differences in biological activities among the samples to differences in the amount of bioactive peptides. The anti-hypertensive peptides VPP and IPP, as well as the DPP-IV-inhibitory peptide APFPE, were quantified. In conclusion, WPC fermentation with S. thermophilus positively impacted protein hydrolysis and bioactive peptide release during GID.
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Osugi, Tomohiro, Katsuhisa Uchida, Masumi Nozaki, and Kazuyoshi Tsutsui. "Characterization of Novel RFamide Peptides in the Central Nervous System of the Brown Hagfish: Isolation, Localization, and Functional Analysis." Endocrinology 152, no. 11 (August 23, 2011): 4252–64. http://dx.doi.org/10.1210/en.2011-1375.
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RFamide (RFa) peptides play various important roles in the central nervous system in both invertebrates and vertebrates. However, there is no evidence of the existence of any RFamide peptide in the brain of hagfish, one of the oldest lineages of vertebrates. In this study, we sought to identify novel RFamide peptides from the brains of hagfish (Paramyxine atami). We identified four novel RFamide peptides, which had the C-terminal Pro-Gln-Arg-Phe-NH2 structure. cDNA cloning revealed that the identified RFamide peptides are encoded in two types of cDNA. Molecular phylogenetic analysis of the two precursors indicated that the hagfish RFamide peptides belong to the PQRFamide peptide group that includes mammalian neuropeptide FF and AF. Based on immunohistochemistry and in situ hybridization, hagfish PQRFamide peptide precursor mRNA and its translated peptides were localized in the infundibular nucleus of the hypothalamus. Immunoreactive fibers were terminated on blood vessels in the infundibular nucleus. Dense immunoreactive fibers were also observed in other brain regions. We further showed that one of the hagfish PQRFamide peptides significantly stimulated the expression of gonadotropin-β mRNA in the cultured hagfish pituitary. These results indicate that the control mechanism of gonadotropin expression by a hypothalamic neuropeptide evolved in the agnathan brain. This is the first evidence describing the identification of RFamide peptides in the hagfish brain. This is also the first report showing the regulation of gonadotropin expression by a homolog of neuropeptide FF that belongs to the PQRFamide peptide group in any vertebrate.
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Yin, Liusong, Mauricio Calvo-Calle, and Lawrence Stern. "Characterization of HLA-DM susceptibility of MHC II-peptide complex in antigen presentation and epitope selection (100.54)." Journal of Immunology 186, no. 1_Supplement (April 1, 2011): 100.54. http://dx.doi.org/10.4049/jimmunol.186.supp.100.54.
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Abstract HLA-DM (DM) is a non-classic major histocompatibility complex II (MHC II), which mediates the exchange of peptides loading to MHC II during antigen presentation. However, the role of DM-mediated peptide exchange in epitope selection is still unclear. In this study, we addressed this question systematically using overlapping peptides from vaccinia virus protein A10L. We measured the binding affinity, intrinsic half life, DM-mediated half life and immunogenecity of 126 A10L peptides bound to HLA-DR1. Correlation coefficient analysis shows that immunogenecity of peptides is very weakly correlated with either binding affinity or intrinsic half life, while strongly correlating with half life in the presence of DM. Moreover, receiver operating characteristics analysis (ROC) indicates that DM-mediated half life is a very strong predictor for epitopes, while binding affinity and intrinsic half life can only mildly predicts epitopes. Taken together, our present quantitative and qualitive analysises demonstrate that DM-susceptibility is a strong and independent factor governing peptide’s immunogenicity.
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Wang, Qin, Yanchao Wang, Xiaoming Jiang, Lei Ma, Zhaojie Li, Yaoguang Chang, Yuming Wang, and Changhu Xue. "Amino Acid Profiling with Chemometric Analysis as a Feasible Tool for the Discrimination of Marine-Derived Peptide Powders." Foods 10, no. 6 (June 4, 2021): 1294. http://dx.doi.org/10.3390/foods10061294.
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Marine-derived peptide powders have suffered from adulteration via the substitution of lower-price peptides or the addition of adulterants in the market. This study aims to establish an effective approach for the discrimination and detection of adulterants for four representative categories of marine-derived peptide powders, namely, oyster peptides, sea cucumber peptides, Antarctic krill peptides, and fish skin peptides, based on amino acid profiling alongside chemometric analysis. The principal component analysis and orthogonal partial least squares discriminant analysis results indicate that four categories of marine-derived peptides could be distinctly classified into four clusters and aggregated with the respective raw materials. Taurine, glycine, lysine, and protein contents were the major discriminants. A reliable classification model was constructed and validated by the prediction dataset, mixture sample dataset, and unclassified sample dataset with accuracy values of 100%, 100%, and 100%, respectively.
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Peng, Zhenghong. "NMR conformational analysis on cyclic decapeptide template molecule." Canadian Journal of Chemistry 77, no. 8 (August 1, 1999): 1394–404. http://dx.doi.org/10.1139/v99-128.
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We report the synthesis and conformational analysis of a series of cyclic and bicyclic decapeptide templates for combinatorial chemistry. The peptides were synthesized via solid phase synthesis and followed by solution cyclization. The conformation of the peptides was studied by proton NMR spectroscopy in DMSO and in TFE-water. The structure of the peptide template was calculated with the program DIANA and followed by SA from the NMR experimental constraints. The peptide adopts a fold comprising two β-strands and two type II β-turns. The design of such a restained cyclic decapeptide template will be discussed along with Template Assembled Synthetic Proteins (TASP).Key words: solid phase peptide synthesis, cyclic decapeptide, NMR, conformational analysis, β-sheet.
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Kusumaningtyas, Eni, R. Widiastuti, H. D. Kusumaningrum, and M. T. Suhartono. "Bioactivities and analysis of peptides from Sumbawa horse milk generated by Bacillus thuringiensis protease." Jurnal Ilmu Ternak dan Veteriner 21, no. 4 (January 11, 2018): 244. http://dx.doi.org/10.14334/jitv.v21i4.1627.
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<p class="abstrak2">Sumbawa horse milk is claimed to cure some diseases such as asthma, hypertension, diabetes and gastrointestinal disorder but its potential bioactive peptide has not been explored. The aims of this study are to evaluate bioactivities peptides from Sumbawa horse milk protein hydrolysate and to analyzethe physio-chemical properties of selected peptides. The milk protein was hydrolyzed by Bacillus thuringiensis protease, the peptide produced were sequential fractionated and then analyzed for antibacterial and antioxidant activities. The peptide fraction <3 kDa was then sequenced using LCMS-MS and the physio-chemical properties of the peptides were analyzed. The result showed that peptides fraction <3 kDa from the 30 min hydrolysis was the most active as antibacterial and more active to Gram negative bacteria. For antioxidant, scavenging activity of the fraction per µg protein/mL were 83% to ABTS and 31% to DPPH radicals. The values were similar with vitamin C 12.5 µg/mL for ABTS and 14.5 µg/mL for DPPH. Peptide <tt>HPYFYAPELLYYANK with molecular weight prediction </tt>1887.92 Da and isoelectric point 7.47 has high therapeutic index prediction (64.75). The result showed that peptides from Sumbawa horse milk hydrolyzed by Bacillus thuringiensis protease was active as antibacterial and antioxidant. Peptide <tt>HPYFYAPELLYYANK from fraction <3 kDa was potential as antibacterial.</tt></p><p><strong>Key Words:</strong> <em>Bacillus thuringiensis</em>, Bioactive Peptide, Horse Milk</p>
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Anusha, G., and M. Monisha. "Molecular modeling and screening of antiviral peptides for Influenza A virus Polymerase basic protein 2(PB2) protein using Hpepdock software for the therapy of Influenza A." CARDIOMETRY, no. 25 (February 14, 2023): 1693–701. http://dx.doi.org/10.18137/cardiometry.2022.25.16931701.
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Aim: To determine the binding affinity (kcal/mol) for various antiviral peptides to target Influenza A virus PB2 protein using Hpepdock software and comparison with the Macrocyclic iHA100 peptide (Reference peptide). Materials and methods: The three-dimensional (3D) coordinates for PB2 protein were retrieved from Protein Data Bank (PDB ID 4P1U). The structures of 16 antiviral peptides were modeled using HPEPDOCK. The Molecular docking analysis of PB2 protein with derived antiviral peptides was performed using Hpepdock software. This software employs an algorithm that generates the output complexes based on the peptide conformations and orientations. Results: Molecular docking analysis revealed that antiviral peptides, P9R Peptide 2, P9R Peptide 3 and P9R Peptide 1, could bind PB2 protein with higher affinity in comparison with the reference Macrocyclic iHA-100 peptide. The antiviral peptides of P9R Peptide 2, P9R Peptide 3 and P9R Peptide 1 with p=0.786, p>0.05 insignificant (-202.728Kcal/mol), p=0.001, p<0.05 significant (-198.255 Kcal/mol), p=0.259, p>0.05 insignificant (-195,788 Kcal/mol) showed better results in comparison to reference Macrocyclic iHA-100 peptide (-154.392 Kcal/ mol). Conclusion: The identified antiviral peptides could more effectively inhibit PB2 protein than the other available peptides on the market to treat Influenza A viral disease.
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He, Ronghai, Haile Ma, Weirui Zhao, Wenjuan Qu, Jiewen Zhao, Lin Luo, and Wenxue Zhu. "Modeling the QSAR of ACE-Inhibitory Peptides with ANN and Its Applied Illustration." International Journal of Peptides 2012 (June 9, 2012): 1–9. http://dx.doi.org/10.1155/2012/620609.
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A quantitative structure-activity relationship (QSAR) model of angiotensin-converting enzyme- (ACE-) inhibitory peptides was built with an artificial neural network (ANN) approach based on structural or activity data of 58 dipeptides (including peptide activity, hydrophilic amino acids content, three-dimensional shape, size, and electrical parameters), the overall correlation coefficient of the predicted versus actual data points is , and the model was applied in ACE-inhibitory peptides preparation from defatted wheat germ protein (DWGP). According to the QSAR model, the C-terminal of the peptide was found to have principal importance on ACE-inhibitory activity, that is, if the C-terminal is hydrophobic amino acid, the peptide's ACE-inhibitory activity will be high, and proteins which contain abundant hydrophobic amino acids are suitable to produce ACE-inhibitory peptides. According to the model, DWGP is a good protein material to produce ACE-inhibitory peptides because it contains 42.84% of hydrophobic amino acids, and structural information analysis from the QSAR model showed that proteases of Alcalase and Neutrase were suitable candidates for ACE-inhibitory peptides preparation from DWGP. Considering higher DH and similar ACE-inhibitory activity of hydrolysate compared with Neutrase, Alcalase was finally selected through experimental study.
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Polak-Berecka, Magdalena, Magdalena Michalak-Tomczyk, Katarzyna Skrzypczak, Katarzyna Michalak, Kamila Rachwał, and Adam Waśko. "Potential Biological Activities of Peptides Generated during Casein Proteolysis by Curly Kale (Brassica oleracea L. var. sabellica L.) Leaf Extract: An In Silico Preliminary Study." Foods 10, no. 11 (November 21, 2021): 2877. http://dx.doi.org/10.3390/foods10112877.
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This study is a brief report on the proteolytic activity of curly kale leaf extract against casein. Casein degradation products and an in silico analysis of the biological activity of the peptides obtained was performed. The efficiency of casein hydrolysis by curly kale extract was determined using SDS–PAGE and by peptide concentration determination. The pattern of the enzymatic activity was determined by MALDI–TOF MS analysis. The results showed that α- and β-casein were more resistant to curly kale extract hydrolysis, whereas κ-casein was absent in the protein profile after 8 h of proteolysis, and all casein fractions were completely hydrolyzed after 24 h of incubation. Based on sequence analysis, seven peptides were identified, with molecular mass in the range of 1151–3024 Da. All the peptides were products of β-casein hydrolysis. The identified amino acid sequences were analyzed in BIOPEP, MBPDB, and FeptideDB databases in order to detect the potential activities of the peptides. In silico analysis suggests that the β-casein-derived peptides possess sequences of peptides with ACE inhibitory, antioxidant, dipeptidyl peptidase IV inhibitory, antithrombotic, immunomodulatory, and antiamnesic bioactivity. Our study was first to evaluate the possibility of applying curly kale leaf extract to generate biopeptides through β-casein hydrolysis.
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Bourganou, Maria V., Evangelos Kontopodis, George Th Tsangaris, Vasileios Pierros, Natalia G. C. Vasileiou, Vasia S. Mavrogianni, George C. Fthenakis, and Angeliki I. Katsafadou. "Unique Peptides of Cathelicidin-1 in the Early Detection of Mastitis—In Silico Analysis." International Journal of Molecular Sciences 24, no. 12 (June 15, 2023): 10160. http://dx.doi.org/10.3390/ijms241210160.
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Based on the results of previously performed clinical studies, cathelicidin-1 has been proposed as a potential biomarker for the early diagnosis of mastitis in ewes. It has been hypothesized that the detection of unique peptides (defined as a peptide, irrespective of its length, that exists in only one protein of a proteome of interest) and core unique peptides (CUPs) (representing the shortest peptide that is unique) of cathelicidin-1 may potentially improve its identification and consequently the diagnosis of sheep mastitis. Peptides of sizes larger than those of the size of CUPs, which include consecutive or over-lapping CUPs, have been defined as ‘composite core unique peptides’ (CCUPs). The primary objective of the present study was the investigation of the sequence of cathelicidin-1 detected in ewes’ milk in order to identify its unique peptides and core unique peptides, which would reveal potential targets for accurate detection of the protein. An additional objective was the detection of unique sequences among the tryptic digest peptides of cathelicidin-1, which would improve accuracy of identification of the protein when performing targeted MS-based proteomics. The potential uniqueness of each peptide of cathelicidin-1 was investigated using a bioinformatics tool built on a big data algorithm. A set of CUPs was created and CCUPs were also searched. Further, the unique sequences in the tryptic digest peptides of cathelicidin-1 were also detected. Finally, the 3D structure of the protein was analyzed from predicted models of proteins. In total, 59 CUPs and four CCUPs were detected in cathelicidin-1 of sheep origin. Among tryptic digest peptides, there were six peptides that were unique in that protein. After 3D structure analysis of the protein, 35 CUPs were found on the core of cathelicidin-1 of sheep origin and among them, 29 were located on amino acids in regions of the protein with ‘very high’ or ‘confident’ estimates of confidence of the structure. Ultimately, the following six CUPs: QLNEQ, NEQS, EQSSE, QSSEP, EDPD, DPDS, are proposed as potential antigenic targets for cathelicidin-1 of sheep. Moreover, another six unique peptides were detected in tryptic digests and offer novel mass tags to facilitate the detection of cathelicidin-1 during MS-based diagnostics.
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Boesen, Agnieszka, Krishnan Sundar, and Richard Coico. "Lassa Fever Virus Peptides Predicted by Computational Analysis Induce Epitope-Specific Cytotoxic-T-Lymphocyte Responses in HLA-A2.1 Transgenic Mice." Clinical Diagnostic Laboratory Immunology 12, no. 10 (October 2005): 1223–30. http://dx.doi.org/10.1128/cdli.12.10.1223-1230.2005.
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ABSTRACT Lassa fever is a hemorrhagic disease caused by Lassa fever virus (LV). Although the precise host defense mechanism(s) that affords protection against LV is not completely understood, cellular immunity mediated by cytotoxic T lymphocytes (CTLs) plays a pivotal role in controlling viral replication and LV infection. To date, there have been no reports mapping major histocompatibility complex (MHC) class I-binding CTL epitopes for LV. Using computer-assisted algorithms, we identified five HLA-A2.1-binding peptides of LV glycoprotein (GP) and two peptides from LV nucleoprotein (NP). Synthesized peptides were examined for their ability to bind to MHC class I molecules using a flow cytometric assay that measures peptide stabilization of class I. Three of the LV-GP peptides tested (LLGTFTWTL, SLYKGVYEL, and YLISIFLHL) stabilized HLA-A2. The LV-NP peptides tested failed to stabilize this HLA-A2. We then investigated the ability of the HLA-A2-binding LV-GP peptides to generate peptide-specific CTLs in HLA-A2.1 transgenic mice. Functional assays used to confirm CTL activation included gamma interferon enzyme-linked immunospot (ELISPOT) assays and intracellular cytokine staining of CD8+ T cells from peptide-primed mice. CTL assays were also performed to verify the cytolytic activity of peptide-pulsed target cells. Each of the LV-GP peptides induced CTL responses in HLA-A2-transgenic mice. MHC class I tetramers prepared using one LV-GP peptide that showed the highest cytolytic index (LLGTFTWTL) confirmed that peptide-binding CD8+ T cells were present in pooled lymphocytes harvested from peptide-primed mice. These findings provide direct evidence for the existence of LV-derived GP epitopes that may be useful in the development of protective immunogens for this hemorrhagic virus.
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Van, Julie A. D., Sergi Clotet-Freixas, Joyce Zhou, Ihor Batruch, Chunxiang Sun, Michael Glogauer, Luca Rampoldi, et al. "Peptidomic Analysis of Urine from Youths with Early Type 1 Diabetes Reveals Novel Bioactivity of Uromodulin Peptides In Vitro." Molecular & Cellular Proteomics 19, no. 3 (December 26, 2019): 501–17. http://dx.doi.org/10.1074/mcp.ra119.001858.
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Chronic hyperglycemia is known to disrupt the proteolytic milieu, initiating compensatory and maladaptive pathways in the diabetic kidney. Such changes in intrarenal proteolysis are captured by the urinary peptidome. To elucidate the early kidney response to chronic hyperglycemia, we conducted a peptidomic investigation into urines from otherwise healthy youths with type 1 diabetes and their non-diabetic peers using unbiased and targeted mass spectrometry-based techniques. This cross-sectional study included two separate cohorts for the discovery (n = 30) and internal validation (n = 30) of differential peptide excretion. Peptide bioactivity was predicted using PeptideRanker and subsequently verified in vitro. Proteasix and the Nephroseq database were used to identify putative proteases responsible for peptide generation and examine their expression in diabetic nephropathy. A total of 6550 urinary peptides were identified in the discovery analysis. We further examined the subset of 162 peptides, which were quantified across all thirty samples. Of the 15 differentially excreted peptides (p < 0.05), seven derived from a C-terminal region (589SGSVIDQSRVLNLGPITRK607) of uromodulin, a kidney-specific protein. Increased excretion of five uromodulin peptides was replicated in the validation cohort using parallel reaction monitoring (p < 0.05). One of the validated peptides (SGSVIDQSRVLNLGPI) activated NFκB and AP-1 signaling, stimulated cytokine release, and enhanced neutrophil migration in vitro. In silico analyses highlighted several potential proteases such as hepsin, meprin A, and cathepsin B to be responsible for generating these peptides. In summary, we identified a urinary signature of uromodulin peptides associated with early type 1 diabetes before clinical manifestations of kidney disease and discovered novel bioactivity of uromodulin peptides in vitro. Our present findings lay the groundwork for future studies to validate peptide excretion in larger and broader populations, to investigate the role of bioactive uromodulin peptides in high glucose conditions, and to examine proteases that cleave uromodulin.
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Kuhn-Nentwig, Lucia, Nicolas Langenegger, Manfred Heller, Dominique Koua, and Wolfgang Nentwig. "The Dual Prey-Inactivation Strategy of Spiders—In-Depth Venomic Analysis of Cupiennius salei." Toxins 11, no. 3 (March 19, 2019): 167. http://dx.doi.org/10.3390/toxins11030167.
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Most knowledge of spider venom concerns neurotoxins acting on ion channels, whereas proteins and their significance for the envenomation process are neglected. The here presented comprehensive analysis of the venom gland transcriptome and proteome of Cupiennius salei focusses on proteins and cysteine-containing peptides and offers new insight into the structure and function of spider venom, here described as the dual prey-inactivation strategy. After venom injection, many enzymes and proteins, dominated by α-amylase, angiotensin-converting enzyme, and cysteine-rich secretory proteins, interact with main metabolic pathways, leading to a major disturbance of the cellular homeostasis. Hyaluronidase and cytolytic peptides destroy tissue and membranes, thus supporting the spread of other venom compounds. We detected 81 transcripts of neurotoxins from 13 peptide families, whereof two families comprise 93.7% of all cysteine-containing peptides. This raises the question of the importance of the other low-expressed peptide families. The identification of a venom gland-specific defensin-like peptide and an aga-toxin-like peptide in the hemocytes offers an important clue on the recruitment and neofunctionalization of body proteins and peptides as the origin of toxins.
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Soltaninejad, Hossein, Hadi Zare-Zardini, Mahtab Ordooei, Yaser Ghelmani, Akram Ghadiri-Anari, Sanaz Mojahedi, and Amir Ali Hamidieh. "Antimicrobial Peptides from Amphibian Innate Immune System as Potent Antidiabetic Agents: A Literature Review and Bioinformatics Analysis." Journal of Diabetes Research 2021 (June 29, 2021): 1–10. http://dx.doi.org/10.1155/2021/2894722.
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Antimicrobial peptides, as an important member of the innate immune system, have various biological activities in addition to antimicrobial activity. There are some AMPs with antidiabetic activity, especially those isolated from amphibians. These peptides can induce insulin release via different mechanisms based on peptide type. In this review study, we collected all reported AMPs with antidiabetic activity. We also analyze the sequence and structure of these peptides for evaluation of sequence and structure effect on their antidiabetic activity. Based on this review, the biggest peptide family with antidiabetic activity is temporins with nine antidiabetic peptides. Frogs are the most abundant source of antidiabetic peptides. Bioinformatics analysis showed that an increase of positive net charge and a decrease of hydrophobicity can improve the insulinotropic effect of peptides. Peptides with higher positive net charge and Boman index showed higher activity. Based on this review article, AMPs with antidiabetic activity, especially those isolated from amphibians, can be used as novel antidiabetic drug for type 2 diabetes disease. So, amphibians are potential sources for active peptides which merit further evaluation as novel insulin secretagogues. However, strategy for the increase of stability and positive activity as well as the decrease of negative side effects must be considered.
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Geetha, R., and R. Padmavathy. "Thermoacoustic, Electrochemical, Solvation and Antimicrobial Analysis of Ternary Potassium Salts Solutions at 308.15K." International Journal of Current Research and Review 15, no. 02 (2023): 16–22. http://dx.doi.org/10.31782/ijcrr.2023.15203.
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Introduction: Amino acids join with each other by peptide bonds and build polymers referred to peptides and proteins. Peptides are recognized for being very therapeutic, selective and comparably safe. As a result, peptides are receiving more attention in pharmaceutical research and development. The scientific progress of ultrasonics has been employed extensively in past decades for both industrial and medical applications. Aim/Objectives: Ultrasonic investigation in non- aqueous solutions of electrolytes with peptides provide information that is helpful in understanding the behaviour of liquids/solutions system. In the present work, the ultrasonic velocity of a peptide with electrolyte in formamide has been measured at various concentrations at 308.15K. Methods: Utilizing the measured data the thermoacoustical, electrochemical and solvation analysis are carried out. The interionic and intermolecular interactions existing in the present system are studied in detail. Conclusion: The results arrived from ultrasonic methods have been corroborated with antimicrobial activity of the samples.
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Tsybin, Youri O., Per Håkansson, Magnus Wetterhall, Karin E. Markides, and Jonas Bergquist. "Capillary Electrophoresis and Electron Capture Dissociation Fourier Transform Ion Cyclotron Resonance Mass Spectrometry for Peptide Mixture and Protein Digest Analysis." European Journal of Mass Spectrometry 8, no. 5 (October 2002): 389–95. http://dx.doi.org/10.1255/ejms.514.
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Recent advances in peptide fragmentation techniques and mass spectrometry have opened up the possibility of combining peptide separation techniques, such as capillary electrophoresis (CE) and capillary liquid chromatography, with Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and electron capture dissociation (ECD) in order to characterize peptide mixtures and protein digests. The results presented in this study show that CE/ECD-FT-ICR MS can be employed for peptide characterization in mixtures of standard peptides and in peptides resulting from the enzymatic digestion of proteins. Furthermore, the technique has potential for the identification and localization of post-translational modifications in peptides and proteins.
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Ma, Chaoyue, Dan Liu, Huifang Hao, and Xiaotong Wu. "Identification of the DPP-IV Inhibitory Peptides from Donkey Blood and Regulatory Effect on the Gut Microbiota of Type 2 Diabetic Mice." Foods 11, no. 14 (July 20, 2022): 2148. http://dx.doi.org/10.3390/foods11142148.
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After being treated with protease K, peptides extracted from donkey blood were separated, identified, and characterized. The results showed that Sephadex G-25 medium purified with MW < 3 kDa had the highest dipeptidyl peptidase IV (DPP-IV) inhibition capacity. Three-hundred-and-thirty-four peptides were identified with UPLC–MS/MS. Peptide Ranker and molecular docking analysis were used to screen active peptides, and 16 peptides were finalized out of the 334. The results showed that the lowest binding energy between P7(YPWTQ) and DPP-IV was −9.1, and the second-lowest binding energy between P1(VDPENFRLL) and DPP-IV was −8.7. The active peptides(MW < 3 kDa) could cause a reduction in the fasting blood glucose levels of type 2 diabetic mice, improve glucose tolerance, and facilitate healing of the damaged structure of diabetic murine liver and pancreas. Meanwhile, the peptides were found to ameliorate the diabetic murine intestinal micro-ecological environment to a certain extent.
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Lee, Joon Ha, Hoyong Chung, Yong Pyo Shin, In-Woo Kim, Sathishkumar Natarajan, Karpagam Veerappan, Minchul Seo, Junhyung Park, and Jae Sam Hwang. "Transcriptome Analysis of Psacothea hilaris: De Novo Assembly and Antimicrobial Peptide Prediction." Insects 11, no. 10 (October 5, 2020): 676. http://dx.doi.org/10.3390/insects11100676.
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Antimicrobial peptides (AMPs) are the frontline innate defense system evolutionarily preserved in insects to combat invading pathogens. These AMPs could serve as an alternative to classical antibiotics to overcome the burden of treating multidrug resistant bacteria. Psacotheasin, a knottin type AMP was isolated from Psacothea hilaris and shown to exhibit antimicrobial activity, especially against fungi through apoptosis mediated cell death. In this study, we aimed to identify novel probable AMPs from Psacothea hilaris, the yellow spotted longicorn beetle. The beetle was immunized with the two bacterial strains (E. coli and S. aureus), and the yeast strain C. albicans. After immunization, total RNA was isolated and sequenced in Illumina platform. Then, beetle transcriptome was de novo assembled and searched for putative AMPs with the known physiochemical features of the AMPs. A selection of AMP candidates were synthesized and tested for antimicrobial activity. Four peptides showed stronger activity against E. coli than the control AMP, melittin while one peptide showed similar activity against S. aureus. Moreover, four peptides and two peptides showed antifungal activity stronger than and similar to melittin, respectively. Collectively one peptide showed both antibacterial and antifungal activity superior to melittin; thus, it provides a potent antimicrobial peptide. All the peptides showed no hemolysis in all the tested concentrations. These results suggest that in silico mining of insects’ transcriptome could be a promising tool to obtain and optimize novel AMPs for human needs.