Journal articles on the topic 'Peptides'
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1
Ng, Sandy Y. M., David J. VanDyke, Bonnie Chaban, John Wu, Yoshika Nosaka, Shin-Ichi Aizawa, and Ken F. Jarrell. "Different Minimal Signal Peptide Lengths Recognized by the Archaeal Prepilin-Like Peptidases FlaK and PibD." Journal of Bacteriology 191, no. 21 (August 28, 2008): 6732–40. http://dx.doi.org/10.1128/jb.00673-09.
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ABSTRACT In Archaea, the preflagellin peptidase (a type IV prepilin-like peptidase designated FlaK in Methanococcus voltae and Methanococcus maripaludis) is the enzyme that cleaves the N-terminal signal peptide from preflagellins. In methanogens and several other archaeal species, the typical flagellin signal peptide length is 11 to 12 amino acids, while in other archaea preflagellins possess extremely short signal peptides. A systematic approach to address the signal peptide length requirement for preflagellin processing is presented in this study. M. voltae preflagellin FlaB2 proteins with signal peptides 3 to 12 amino acids in length were generated and used as a substrate in an in vitro assay utilizing M. voltae membranes as an enzyme source. Processing by FlaK was observed in FlaB2 proteins containing signal peptides shortened to 5 amino acids; signal peptides 4 or 3 amino acids in length were unprocessed. In the case of Sulfolobus solfataricus, where the preflagellin peptidase PibD has broader substrate specificity, some predicted substrates have predicted signal peptides as short as 3 amino acids. Interestingly, the shorter signal peptides of the various mutant FlaB2 proteins not processed by FlaK were processed by PibD, suggesting that some archaeal preflagellin peptidases are likely adapted toward cleaving shorter signal peptides. The functional complementation of signal peptidase activity by FlaK and PibD in an M. maripaludis ΔflaK mutant indicated that processing of preflagellins was detected by complementation with either FlaK or PibD, yet only FlaK-complemented cells were flagellated. This suggested that a block in an assembly step subsequent to signal peptide removal occurred in the PibD complementation.
2
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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Liu, Yu, Jeffrey A. Sigman, Lisa A. Bruce, and Adele J. Wolfson. "Thimet Oligopeptidase—A Classical Enzyme with New Function and New Form." Immuno 1, no. 4 (September 23, 2021): 332–46. http://dx.doi.org/10.3390/immuno1040022.
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Peptidases generate bioactive peptides that can regulate cell signaling and mediate intercellular communication. While the processing of peptide precursors is initiated intracellularly, some modifications by peptidases may be conducted extracellularly. Thimet oligopeptidase (TOP) is a peptidase that processes neuroendocrine peptides with roles in mood, metabolism, and immune responses, among other functions. TOP also hydrolyzes angiotensin I to angiotensin 1–7, which may be involved in the pathophysiology of COVID-19 infection. Although TOP is primarily cytosolic, it can also be associated with the cell plasma membrane or secreted to the extracellular space. Recent work indicates that membrane-associated TOP can be released with extracellular vesicles (EVs) to the extracellular space. Here we briefly summarize the enzyme’s classical function in extracellular processing of neuroendocrine peptides, as well as its more recently understood role in intracellular processing of various peptides that impact human diseases. Finally, we discuss new findings of EV-associated TOP in the extracellular space.
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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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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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ANDERSON, John W., Suara A. ADEDIRAN, Paulette CHARLIER, Martine NGUYEN-DISTÈCHE, Jean-Marie FRÈRE, Robert A. NICHOLAS, and Rex F. PRATT. "On the substrate specificity of bacterial DD-peptidases: evidence from two series of peptidoglycan-mimetic peptides." Biochemical Journal 373, no. 3 (August 1, 2003): 949–55. http://dx.doi.org/10.1042/bj20030217.
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The reactions between bacterial DD-peptidases and β-lactam antibiotics have been studied for many years. Less well understood are the interactions between these enzymes and their natural substrates, presumably the peptide moieties of peptidoglycan. In general, remarkably little activity has previously been demonstrated in vitro against potential peptide substrates, although in many cases the peptides employed were non-specific and not homologous with the relevant peptidoglycan. In this paper, the specificity of a panel of DD-peptidases against elements of species-specific d-alanyl-d-alanine peptides has been assessed. In two cases, those of soluble, low-molecular-mass DD-peptidases, high activity against the relevant peptides has been demonstrated. In these cases, the high specificity is towards the free N-terminus of the peptidoglycan fragment. With a number of other enzymes, particularly high-molecular-mass DD-peptidases, little or no activity against these peptides was observed. In separate experiments, the reactivity of the enzymes against the central, largely invariant, peptide stem was examined. None of the enzymes surveyed showed high activity against this structural element although weak specificity in the expected direction towards the one structural variable (d-γGln versus d-γGlu) was observed. The current state of understanding of the activity of these enzymes in vitro is discussed.
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Sawada, Toshiki, Rina Oyama, Michihiro Tanaka, and Takeshi Serizawa. "Discovery of Surfactant-Like Peptides from a Phage-Displayed Peptide Library." Viruses 12, no. 12 (December 15, 2020): 1442. http://dx.doi.org/10.3390/v12121442.
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Peptides with specific affinities for various materials have been identified in the past three decades and utilized in materials science and engineering. A peptide’s capability to specifically interact with materials is not naturally derived but screened from a biologically constructed peptide library displayed on phages or cells. To date, due to limitations in the screening procedure, the function of screened peptides has been primarily limited to the affinity for target materials. Herein, we demonstrated the screening of surfactant-like peptides from a phage-displayed peptide library. A screened phage clone displaying a peptide showed high activity for accumulating at emulsion surfaces with certain assembled structures, resulting in stable emulsions. The surface tension for the solution of the chemically synthesized peptide decreased with increasing peptide concentration, demonstrating certain surface activity, which corresponded to the ability to decrease the surface tension of liquids (e.g., water), owing to the accumulation of molecules at the air–liquid or liquid–liquid interface. Peptides with a randomized sequence did not lower the surface tension, indicating the essential role of amino acid sequences in surface activity. Our strategy for identifying novel functional peptides from a phage-displayed peptide library can be used to expand the applicability of peptidyl materials and biosurfactants.
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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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Ting, Yi Tian, Paul W. R. Harris, Gaelle Batot, Margaret A. Brimble, Edward N. Baker, and Paul G. Young. "Peptide binding to a bacterial signal peptidase visualized by peptide tethering and carrier-driven crystallization." IUCrJ 3, no. 1 (January 1, 2016): 10–19. http://dx.doi.org/10.1107/s2052252515019971.
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Bacterial type I signal peptidases (SPases) are membrane-anchored serine proteases that process the signal peptides of proteins exported via the Sec and Tat secretion systems. Despite their crucial importance for bacterial virulence and their attractiveness as drug targets, only one such enzyme, LepB from Escherichia coli, has been structurally characterized, and the transient nature of peptide binding has stymied attempts to directly visualize SPase–substrate complexes. Here, the crystal structure of SpsB, the type I signal peptidase from the Gram-positive pathogen Staphylococcus aureus, is reported, and a peptide-tethering strategy that exploits the use of carrier-driven crystallization is described. This enabled the determination of the crystal structures of three SpsB–peptide complexes, both with cleavable substrates and with an inhibitory peptide. SpsB–peptide interactions in these complexes are almost exclusively limited to the canonical signal-peptide motif Ala-X-Ala, for which clear specificity pockets are found. Minimal contacts are made outside this core, with the variable side chains of the peptides accommodated in shallow grooves or exposed faces. These results illustrate how high fidelity is retained despite broad sequence diversity, in a process that is vital for cell survival.
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Leszczyńska, Joanna, Agnieszka K. Szczepankowska, Iwona Majak, Dorota Mańkowska, Beata Smolińska, Sylwia Ścieszka, Anna Diowksz, Bożena Cukrowska, and Tamara Aleksandrzak-Piekarczyk. "Reducing Immunoreactivity of Gluten Peptides by Probiotic Lactic Acid Bacteria for Dietary Management of Gluten-Related Diseases." Nutrients 16, no. 7 (March 27, 2024): 976. http://dx.doi.org/10.3390/nu16070976.
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Immunoreactive gluten peptides that are not digested by peptidases produced by humans can trigger celiac disease, allergy and non-celiac gluten hypersensitivity. The aim of this study was to evaluate the ability of selected probiotic strains to hydrolyze immunoreactive gliadin peptides and to identify peptidase-encoding genes in the genomes of the most efficient strains. Residual gliadin immunoreactivity was measured after one- or two-step hydrolysis using commercial enzymes and bacterial peptidase preparations by G12 and R5 immunoenzymatic assays. Peptidase preparations from Lacticaseibacillus casei LC130, Lacticaseibacillus paracasei LPC100 and Streptococcus thermophilus ST250 strains significantly reduced the immunoreactivity of gliadin peptides, including 33-mer, and this effect was markedly higher when a mixture of these strains was used. In silico genome analyses of L. casei LC130 and L. paracasei LPC100 revealed the presence of genes encoding peptidases with the potential to hydrolyze bonds in proline-rich peptides. This suggests that L. casei LC130, L. paracasei LPC100 and S. thermophilus ST250, especially when used as a mixture, have the ability to hydrolyze immunoreactive gliadin peptides and could be administered to patients on a restricted gluten-free diet to help treat gluten-related diseases.
11
Hwang, Peter M., and Hans J. Vogel. "Structure-function relationships of antimicrobial peptides." Biochemistry and Cell Biology 76, no. 2-3 (May 1, 1998): 235–46. http://dx.doi.org/10.1139/o98-026.
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Antimicrobial peptides are ubiquitously produced throughout nature. Many of these relatively short peptides (6-50 residues) are lethal towards bacteria and fungi, yet they display minimal toxicity towards mammalian cells. All of the peptides are highly cationic and hydrophobic. It is widely believed that they act through nonspecific binding to biological membranes, even though the exact nature of these interactions is presently unclear. High-resolution nuclear magnetic resonance (NMR) has contributed greatly to knowledge in this field, providing insight about peptide structure in aqueous solution, in organic cosolvents, and in micellar systems. Solid-state NMR can provide additional information about peptide-membrane binding. Here we review our current knowledge about the structure of antimicrobial peptides. We also discuss studies pertaining to the mechanism of action. Despite the different three-dimensional structural motifs of the various classes, they all have similar amphiphilic surfaces that are well-suited for membrane binding. Many antimicrobial peptides bind in a membrane-parallel orientation, interacting only with one face of the bilayer. This may be sufficient for antimicrobial action. At higher concentrations, peptides and phospholipids translocate to form multimeric transmembrane channels that seem to contribute to the peptide's hemolytic activity. An understanding of the key features of the secondary and tertiary structures of the antimicrobial peptides and their effects on bactericidal and hemolytic activity can aid the rational design of improved analogs for clinical use.Key words: structure, antimicrobial peptide, NMR, membrane, hemolytic.
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Shinde, Ujwal P. "Can the topological distribution of membrane spanning amino acid residues be responsible for the recognition of signal peptides by signal peptide peptidases?" Bioscience Reports 10, no. 6 (December 1, 1990): 537–46. http://dx.doi.org/10.1007/bf01116614.
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Signal peptides are selectively recognized and degraded by membrane associated proteases called as signal peptide peptidases. The hydrolysis of the signal peptide occurs only after its cleavage from the precursor. The possible reasons for this selectivity have been investigated. The results indicate that in signal peptides, leucine residues are clustered to a large extent on the same side of the membrane spanning alpha helix as the polar residues, but are distinctly separated along the length of the axis. Such topological differences in the distribution of amino acids on the surface of the membrane spanning alpha helix may play a crucial role in selective degradation of signal peptides.
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Purcell, Diane, Michael A. Packer, and Maria Hayes. "Identification of Bioactive Peptides from a Laminaria digitata Protein Hydrolysate Using In Silico and In Vitro Methods to Identify Angiotensin-1-Converting Enzyme (ACE-1) Inhibitory Peptides." Marine Drugs 21, no. 2 (January 27, 2023): 90. http://dx.doi.org/10.3390/md21020090.
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Bioactive peptides range in size from 2–30 amino acids and may be derived from any protein-containing biomass using hydrolysis, fermentation or high-pressure processing. Pro-peptides or cryptides result in shorter peptide sequences following digestion and may have enhanced bioactivity. Previously, we identified a protein hydrolysate generated from Laminaria digitata that inhibited ACE-1 in vitro and had an ACE-1 IC50 value of 590 µg/mL compared to an ACE-1 IC50 value of 500 µg/mL (~2.3 µM) observed for the anti-hypertensive drug Captopril©. A number of peptide sequences (130 in total) were identified using mass spectrometry from a 3 kDa permeate of this hydrolysate. Predicted bioactivities for these peptides were determined using an in silico strategy previously published by this group utilizing available databases including Expasy peptide cutter, BIOPEP and Peptide Ranker. Peptide sequences YIGNNPAKGGLF and IGNNPAKGGLF had Peptide Ranker scores of 0.81 and 0.80, respectively, and were chemically synthesized. Synthesized peptides were evaluated for ACE-1 inhibitory activity in vitro and were found to inhibit ACE-1 by 80 ± 8% and 91 ± 16%, respectively. The observed ACE-1 IC50 values for IGNNPAKGGLF and YIGNNPAKGGLF were determined as 174.4 µg/mL and 133.1 µg/mL. Both peptides produced sequences following simulated digestion with the potential to inhibit Dipeptidyl peptidase IV (DPP-IV).
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Ganapathy, V., and F. H. Leibach. "Carrier-mediated reabsorption of small peptides in renal proximal tubule." American Journal of Physiology-Renal Physiology 251, no. 6 (December 1, 1986): F945—F953. http://dx.doi.org/10.1152/ajprenal.1986.251.6.f945.
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Recent studies with a variety of tissue preparations in the kidney have demonstrated that proximal tubular cells possess specific transport systems for di- and tripeptides. In contrast to the well-known amino acid and glucose transport systems, active transport of peptides in these cells is energized by an H+ gradient rather than an Na+ gradient. Like amino acid-Na+ and glucose-Na+ cotransport systems, peptide-H+ cotransport is electrogenic and hence a membrane potential also contributes to the uphill transport of peptides in these cells. Di- and tripeptides that are filtered at the glomerulus, as well as those that are produced in the tubular lumen from larger polypeptides by the action of brush-border peptidases, serve as substrates for the renal peptide transport system under physiological conditions. The H+ gradient that is necessary to drive renal peptide transport is generated in vivo by concerted action of the basolateral Na+-K+-ATPase and the brush-border Na+-H+ exchanger. The peptidases and the peptide transport system in the renal brush-border membrane play a significant role in the reabsorption of peptide-bound amino acids as well as in the regulation of plasma levels of small peptides.
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Ulyanova, Vera, Elena Dudkina, Alsu Nadyrova, Vladimir Kalashnikov, Yulia Surchenko, and Olga Ilinskaya. "The Cytotoxicity of RNase-Derived Peptides." Biomolecules 11, no. 1 (December 26, 2020): 16. http://dx.doi.org/10.3390/biom11010016.
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Bacterial ribonuclease binase exhibits a cytotoxic effect on tumor cells possessing certain oncogenes. The aim of this study was to identify the structural parts of the binase molecule that exert cytotoxicity. Out of five designed peptides, the peptides representing the binase regions 21–50 and 74–94 have the highest cytotoxic potential toward human cervical HeLa and breast BT-20 and MCF-7 cancer cells. The peptides B21–50 and B74–94 were not able to enter human lung adenocarcinoma A549 cells, unlike BT-20 cells, explaining their failure to inhibit A549 cell proliferation. The peptide B74–94 shares similarities with epidermal growth factor (EGF), suggesting the peptide’s specificity for EGF receptor overexpressed in BT-20 cells. Thus, the binase-derived peptides have the potential of being further developed as tumor-targeting peptides.
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Shi, Yu, Chunwu Yu, and Wentao Ma. "Towards an RNA/Peptides World by the Direct RNA Template Mechanism: The Emergence of Membrane-Stabilizing Peptides in RNA-Based Protocells." Life 13, no. 2 (February 14, 2023): 523. http://dx.doi.org/10.3390/life13020523.
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How functional peptides may have arisen is a significant problem for the scenario of the RNA world. An attractive idea, the direct RNA template (DRT) hypothesis, proposes that RNA molecules can bind amino acids specifically and promote the synthesis of corresponding peptides, thereby starting the RNA/peptides world. To investigate the plausibility of this idea, we modeled the emergence of a “membrane-stabilizing peptide” in RNA-based protocells—such a peptide was suggested to have appeared early in the RNA world based on experimental evidence. The computer simulation demonstrated that the protocells containing the “RNA gene” encoding this peptide may spread in the system owing to the peptide’s function. The RNA gene may either originate de novo in protocells or emerge in protocells already containing ribozymes—here we adopt a nucleotide synthetase ribozyme as an example. Furthermore, interestingly, we show that a “nucleotide synthetase peptide” encoded by RNA (also via the DRT mechanism) may substitute the nucleotide synthetase ribozyme in evolution, which may represent how “functional-takeover” in the RNA world could have occurred. Overall, we conclude that the transition from the RNA world towards an RNA/peptides world may well have been mediated by the DRT mechanism. Remarkably, the successful modeling on the emergence of membrane-stabilizing peptide in RNA-based protocells is per se significant, which may imply a “promising” way for peptides to enter the RNA world, especially considering the weak interaction between RNA and the membrane in chemistry.
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Faucher, Mélanie, Thibaud R. Geoffroy, Jacinthe Thibodeau, Sami Gaaloul, and Laurent Bazinet. "Semi-Industrial Production of a DPP-IV and ACE Inhibitory Peptide Fraction from Whey Protein Concentrate Hydrolysate by Electrodialysis with Ultrafiltration Membrane." Membranes 12, no. 4 (April 9, 2022): 409. http://dx.doi.org/10.3390/membranes12040409.
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The separation by electrodialysis with ultrafiltration membranes (EDUF), at a semi-industrial scale, of a new whey protein hydrolysate obtained from a whey protein concentrate was assessed. After 6 h of treatment, more than 9 g of peptides were recovered in the peptide recovery fraction, for a recovery yield of 5.46 ± 0.56% and containing 18 major components. Among these components, positively charged peptides, such as ALPMHIR + PHMIR, LIVTQTMK and TKIPAVF, were present, and their relative abundances increased by nearly 1.25 X and up to 7.55 X. The presence of these peptides may be promising, as ALPMHIR has a strong activity against angiotensin-converting enzyme (ACE), and LIVTQTMK has structural properties that could interfere with dipeptidyl peptidase-IV (DPP-IV). Many neutral peptides were also recovered alongside those. Nevertheless, the inhibitory activity against DPP-IV and ACE increased from 2 X and 4 X, respectively, in the peptide recovery fraction compared to the initial hydrolysate, due to the improved content in bioactive peptides. Thus, this new hydrolysate is well-suited for the large-scale production of a peptide fraction with high bioactivities. Furthermore, what was achieved in this work came close to what could be achieved for the industrial production of a bioactive peptide fraction from whey proteins.
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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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Morozov, Giora, Huaying Zhao, Michael Mage, Lisa Boyd, Ramesh Venna, Michael Norcross, Curtis McMurtrey, et al. "Direct interaction of recombinant TAPBPR with MHC-I molecules: stabilization of peptide-free MHC-I promotes high affinity peptide loading (APP5P.102)." Journal of Immunology 194, no. 1_Supplement (May 1, 2015): 183.4. http://dx.doi.org/10.4049/jimmunol.194.supp.183.4.
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Abstract The loading of MHC-I molecules with peptides for cell surface display is a crucial step in self-tolerance and activation of CD8 T cells. We studied TAPBPR (TAP binding protein-related) protein, a tapasin homolog, which is widely expressed and IFN-γ inducible, but is not part of the classical MHC-I peptide-loading complex. We produced recombinant soluble TAPBPR and evaluated its interactions with several recombinant MHC-I molecules in vitro, by gel-shift, size exclusion chromatography, ultracentrifugation, and surface plasmon resonance. We show that TAPBPR binds MHC-I after photolysis of a bound peptide, and that the TAPBPR/MHC-I complex is dissociated by exposure to peptides that bind the MHC-I molecule, indicating a role of TAPBPR in stabilizing a peptide-receptive form of the MHC-I/β2m complex. Peptide-dependent release of MHC-I from TAPBPR is directly proportional to the peptide’s affinity for MHC-I. Peptide binding experiments indicate a role for TAPBPR in selection of high affinity peptides. Mutagenesis of TAPBPR and MHC-I confirm the importance of amino acid residues conserved with the putative tapasin/MHC-I binding site and reveal additional residues important for the TAPBPR/MHC-I interaction. Molecular docking simulations suggest a detailed mechanism for the interaction of TAPBPR with peptide free MHC-I. These studies are consistent with the view that TAPBPR functions as a chaperone that stabilizes peptide-free MHC-I to permit binding of high affinity peptides.
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Mora-Melgem, José Antonio, Jesús Gilberto Arámburo-Gálvez, Feliznando Isidro Cárdenas-Torres, Jhonatan Gonzalez-Santamaria, Giovanni Isaí Ramírez-Torres, Aldo Alejandro Arvizu-Flores, Oscar Gerardo Figueroa-Salcido, and Noé Ontiveros. "Dipeptidyl Peptidase IV Inhibitory Peptides from Chickpea Proteins (Cicer arietinum L.): Pharmacokinetics, Molecular Interactions, and Multi-Bioactivities." Pharmaceuticals 16, no. 8 (August 4, 2023): 1109. http://dx.doi.org/10.3390/ph16081109.
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Chickpea (Cicer arietinum L.) peptides can inhibit dipeptidyl peptidase IV (DPP-IV), an important type 2 diabetes mellitus therapeutic target. The molecular interactions between the inhibitory peptides and the active site of DPP-IV have not been thoroughly examined, nor have their pharmacokinetic properties. Therefore, the predictions of legumin- and provicilin-derived DPP-IV inhibitory peptides, their molecular interactions with the active site of DPP-IV, and their pharmacokinetic properties were carried out. Ninety-two unique DPP-IV inhibitory peptides were identified. Papain and trypsin were the enzymes with the highest AE (0.0927) and lowest BE (6.8625 × 10−7) values, respectively. Peptide binding energy values ranged from −5.2 to −7.9 kcal/mol. HIS-PHE was the most potent DPP-IV inhibitory peptide and interacts with residues of the active sites S1 (TYR662) and S2 (GLU205/ARG125 (hydrogen bonds: <3.0 Å)), S2 (GLU205/GLU206 (electrostatic interactions: <3.0 Å)), and S2′ pocket (PHE357 (hydrophobic interaction: 4.36 Å)). Most peptides showed optimal absorption (76.09%), bioavailability (89.13%), and were non-toxic (97.8%) stable for gastrointestinal digestion (73.9%). Some peptides (60.86%) could also inhibit ACE-I. Chickpea is a source of non-toxic and bioavailable DPP-IV-inhibitory peptides with dual bioactivity. Studies addressing the potential of chickpea peptides as therapeutic or adjunct agents for treating type 2 diabetes are warranted.
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Nong, Nhung Thi Phuong, and Jue-Liang Hsu. "Characteristics of Food Protein-Derived Antidiabetic Bioactive Peptides: A Literature Update." International Journal of Molecular Sciences 22, no. 17 (September 1, 2021): 9508. http://dx.doi.org/10.3390/ijms22179508.
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Diabetes, a glucose metabolic disorder, is considered one of the biggest challenges associated with a complex complication of health crises in the modern lifestyle. Inhibition or reduction of the dipeptidyl peptidase IV (DPP-IV), alpha-glucosidase, and protein-tyrosine phosphatase 1B (PTP-1B) enzyme activities or expressions are notably considered as the promising therapeutic strategies for the management of type 2 diabetes (T2D). Various food protein-derived antidiabetic bioactive peptides have been isolated and verified. This review provides an overview of the DPP-IV, PTP-1B, and α-glucosidase inhibitors, and updates on the methods for the discovery of DPP-IV inhibitory peptides released from food-protein hydrolysate. The finding of novel bioactive peptides involves studies about the strategy of separation fractionation, the identification of peptide sequences, and the evaluation of peptide characteristics in vitro, in silico, in situ, and in vivo. The potential of bioactive peptides suggests useful applications in the prevention and management of diabetes. Furthermore, evidence of clinical studies is necessary for the validation of these peptides’ efficiencies before commercial applications.
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Wang, P., G. Gyllner, and S. Kvist. "Selection and binding of peptides to human transporters associated with antigen processing and rat cim-a and -b." Journal of Immunology 157, no. 1 (July 1, 1996): 213–20. http://dx.doi.org/10.4049/jimmunol.157.1.213.
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Abstract Cytotoxic T lymphocytes recognize antigenic peptides presented by MHC class I molecules. The peptides are generated in the cytosol by proteasomes, and probably also other proteases, and are then translocated into the endoplasmic reticulum (ER) lumen. The transporters associated with Ag processing (TAP) are key molecules for transporting peptides from the cytosol to the lumen of the ER. Using semipermeabilized cells, TAP-dependent peptide translocation was demonstrated, and the selectivity of peptide translocation was based on the carboxyl-terminal amino acid of peptides. We have examined peptide binding proteins in the ER membrane and the selection of peptides for binding to TAP by using a panel of peptides of different sequences and carboxyl-termini as well as peptides containing D amino acids. Peptides bound to TAP molecules in the absence of ATP. The presence of ATP induced binding of peptides to two additional membrane proteins (58 and 43 kDa). The selection of peptides by TAP molecules was based on peptide sequence and the carboxyl-terminal amino acid. Peptides containing D amino acid did not bind to TAP molecules. Rat cim-a and -b selected peptides differently, and selection was not only dependent on the carboxyl-terminal residue of the peptide, but included an influence of the peptide sequence. The different off-rates after peptide binding to TAP, indicated a dual binding step of peptide to TAP. ATP regulated the off-rate of peptides at a high affinity binding step. Our results demonstrate that the binding of peptides to TAP molecules is specific and most likely involves a multiple step pathway.
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Sridhar, Vidya R., Joanne E. Hughes, Dennis L. Welker, Jeffery R. Broadbent, and James L. Steele. "Identification of Endopeptidase Genes from the Genomic Sequence of Lactobacillus helveticus CNRZ32 and the Role of These Genes in Hydrolysis of Model Bitter Peptides." Applied and Environmental Microbiology 71, no. 6 (June 2005): 3025–32. http://dx.doi.org/10.1128/aem.71.6.3025-3032.2005.
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ABSTRACT Genes encoding three putative endopeptidases were identified from a draft-quality genome sequence of Lactobacillus helveticus CNRZ32 and designated pepO3, pepF, and pepE2. The ability of cell extracts from Escherichia coli DH5α derivatives expressing CNRZ32 endopeptidases PepE, PepE2, PepF, PepO, PepO2, and PepO3 to hydrolyze the model bitter peptides, β-casein (β-CN) (f193-209) and αS1-casein (αS1-CN) (f1-9), under cheese-ripening conditions (pH 5.1, 4% NaCl, and 10°C) was examined. CNRZ32 PepO3 was determined to be a functional paralog of PepO2 and hydrolyzed both peptides, while PepE and PepF had unique specificities towards αS1-CN (f1-9) and β-CN (f193-209), respectively. CNRZ32 PepE2 and PepO did not hydrolyze either peptide under these conditions. To demonstrate the utility of these peptidases in cheese, PepE, PepO2, and PepO3 were expressed in Lactococcus lactis, a common cheese starter, using a high-copy vector pTRKH2 and under the control of the pepO3 promoter. Cell extracts of L. lactis derivatives expressing these peptidases were used to hydrolyze β-CN (f193-209) and αS1-CN (f1-9) under cheese-ripening conditions in single-peptide reactions, in a defined peptide mix, and in Cheddar cheese serum. Peptides αS1-CN (f1-9), αS1-CN (f1-13), and αS1-CN (f1-16) were identified from Cheddar cheese serum and included in the defined peptide mix. Our results demonstrate that in all systems examined, PepO2 and PepO3 had the highest activity with β-CN (f193-209) and αS1-CN (f1-9). Cheese-derived peptides were observed to affect the activity of some of the enzymes examined, underscoring the importance of incorporating such peptides in model systems. These data indicate that L. helveticus CNRZ32 endopeptidases PepO2 and PepO3 are likely to play a key role in this strain's ability to reduce bitterness in cheese.
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Boucau, Julie, Julien Madouasse, Christopher Carlin, Tom Zhu, Yang Xu, Mariko Shimada, and Sylvie Le Gall. "Effect of cellular activation on the antigen processing machinery of primary CD4 T cells. (P5029)." Journal of Immunology 190, no. 1_Supplement (May 1, 2013): 110.15. http://dx.doi.org/10.4049/jimmunol.190.supp.110.15.
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Abstract The killing of HIV-infected CD4 T cells by specific CD8 T cells (CTL) requires the presentation of peptide-MHC-I complexes produced during the intracellular degradation of viral proteins by the proteasome and other peptidases, to their cognate T cell receptors. HIV infection induces general cellular activation, which renders cells more susceptible to infection. Whether the activation state of cells alters the expression and activity of the antigen processing machinery and the kinetics and nature of epitopes displayed by MHC-I is not known despite its potential role in altering the efficiency of recognition of infected cells by CTL. We compared the expression and peptidase activities of the antigen processing machinery of primary CD4 T cells upon activation with anti-CD3/CD28 beads or with phytohemagglutinin. In primary CD4 T cells from HIV seronegative individuals, the hydrolytic activities of the proteasome, the expression of several of its subunits and of the peptidase TPP2 significantly increased upon activation. The mass spectrometry analysis of in vitro degradation of 2 long epitope-containing HIV peptides in extracts from CD3/CD28-activated CD4 T cells showed production of smaller and less antigenic peptides than in the non-activated samples. Reduced presentation of peptides by activated cells might lead to reduced recognition and slower clearance of activated infected cells by CTL thus allowing more time for viral replication and spread.
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Hayes, Maria, Azza Naik, Leticia Mora, Bruno Iñarra, Jone Ibarruri, Carlos Bald, Thibault Cariou, et al. "Generation, Characterisation and Identification of Bioactive Peptides from Mesopelagic Fish Protein Hydrolysates Using In Silico and In Vitro Approaches." Marine Drugs 22, no. 7 (June 27, 2024): 297. http://dx.doi.org/10.3390/md22070297.
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This study generated bioactive hydrolysates using the enzyme Alcalase and autolysis from mesopelagic fish, including Maurolicus muelleri and Benthosema glaciale. Generated hydrolysates were investigated for their bioactivities using in vitro bioassays, and bioactive peptides were identified using mass spectrometry in active hydrolysates with cyclooxygenase, dipeptidyl peptidase IV and antioxidant activities. In silico analysis was employed to rank identified peptide sequences in terms of overall bioactivity using programmes including Peptide Ranker, PrepAIP, Umami-MRNN and AntiDMPpred. Seven peptides predicted to have anti-inflammatory, anti-type 2 diabetes or Umami potential using in silico strategies were chemically synthesised, and their anti-inflammatory activities were confirmed using in vitro bioassays with COX-1 and COX-2 enzymes. The peptide QCPLHRPWAL inhibited COX-1 and COX-2 by 82.90% (+/−0.54) and 53.84%, respectively, and had a selectivity index greater than 10. This peptide warrants further research as a novel anti-inflammatory/pain relief peptide. Other peptides with DPP-IV inhibitory and Umami flavours were identified. These offer potential for use as functional foods or topical agents to prevent pain and inflammation.
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Kadel, Sabita, Geneviève Pellerin, Jacinthe Thibodeau, Véronique Perreault, Carole Lainé, and Laurent Bazinet. "How Molecular Weight Cut-Offs and Physicochemical Properties of Polyether Sulfone Membranes Affect Peptide Migration and Selectivity during Electrodialysis with Filtration Membranes." Membranes 9, no. 11 (November 13, 2019): 153. http://dx.doi.org/10.3390/membranes9110153.
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Filtration membranes (FMs) are an integral part of electrodialysis with filtration membranes (EDFM), a green and promising technology for bioactive peptide fractionation. Therefore, it is paramount to understand how physicochemical properties of FMs impact global and selective peptide migration to anionic (A−RC) and cationic (C+RC) peptide recovery compartments during their simultaneous separation by EDFM. In this context, six polyether sulfone (PES) membranes with molecular weight cut-offs (MWCO) of 5, 10, 20, 50, 100 and 300 kDa were characterized and used during EDFM to separate peptides from a complex whey protein hydrolysate. Surface charge, roughness, thickness and surface/pores nature of studied PES membranes were similar with small differences in conductivity, porosity and pore size distribution. Interestingly, global peptides migration to both recovery compartments increased linearly as a function of MWCO. However, peptide selectivity changed according to the recovery compartments and/or the peptide’s charge and MW with an increase in MWCO of FMs. Indeed, in A−RC, the relative abundance (RA) of peptides having low negative charge and MW (IDALNENK and VLVLDTDYK) decreased (45% to 19%) with an increase in MWCO, while the opposite for peptides having high negative charge and MW (TPEVDDEALEK, TPEVDDEALEKFDK & VYVEELKPTPEGDLEILLQK) (increased from 16% to 43%). Concurrently, in C+RC, regardless of MWCO used, the highest RA was observed for peptides having low positive charge and MW (IPAVFK & ALPMHIR). It was the first time that the significant impact of charge, MWCO and pore size distribution of PES membranes on a wide range of MWCO was demonstrated on EDFM performances.
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Rughani, Ronak V., and Joel P. Schneider. "Molecular Design of β-Hairpin Peptides for Material Construction." MRS Bulletin 33, no. 5 (May 2008): 530–35. http://dx.doi.org/10.1557/mrs2008.106.
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AbstractSelf-assembled materials composed of β-sheet forming peptides hold promise as therapeutics and novel biomaterials. This article focuses on the design and engineering of amphiphilic peptide sequences, especially β-hairpins. Peptides can be designed to intramolecularly fold and then self-assemble on cue, affording hydrogels rich in β-sheet structure. Hydrogels having distinct material properties can be designed at the molecular level by modulating either the peptide's sequence or the environmental stimulus used to trigger folding and assembly, leading to gelation.
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Provenzano, Maurizio, Simone Mocellin, Francesco M. Marincola, and David F. Stroncek. "The Use of Algorithms with a Novel Score Standardization Method for the Selection of Candidate Immunogenic HLA-Specific Peptides Led to the Identification of New Immunogenic HLA-A*0201 Cytomegalovirus Epitopes." Blood 104, no. 11 (November 16, 2004): 2862. http://dx.doi.org/10.1182/blood.v104.11.2862.2862.
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Abstract The identification of HLA class I restricted epitopes within immunogenic proteins that are capable of stimulating memory T lymphocytes is an important step for both clinical vaccine and adoptive immunotherapy. Despite the strong immunogenicity demonstrated by specific HLA restricted peptides, the peptide’s affinity to a specific HLA antigen may vary among individuals. Therefore, it is important to identify more than one immune determinant for each HLA antigen of interest. Two computer algorithms, one by Parker and another by Rammensee, are widely used in immunogenetic studies in order to predict which peptides bind best to specific HLA molecules. The use of these algorithms represents the first step in screening proteins. Parker’s algorithm ranks potential peptide according to the predictive half-time disassociation of peptide/MHC complexes. Rammensee’s algorithm ranks the peptides based on the presence of primary and secondary HLA-binding anchor residues. Starting with the sequence of Cytomegalovirus (CMV) phosphorylated matrix protein 65 (pp65; SwissProt ID: P06725), we derived from each algorithm a list of 250 nonamer (9-mer) peptides predicted to bind to the HLA-A*0201 allele. Standardizing the two groups of scores, corresponding to the endpoints of the stated interval, by the following formula: [(peptide score - mean of scores)/ standard deviation of scores], we obtained pure values that are independent of the unit of measurement, therefore homogeneous and thus comparable. This allowed us to link each peptide to a pair of values, one for each algorithm. The values derived from standardized Parker scores (X axis) were plotted against the values derived from standardized Rammensee scores (Y axis). We represented final results by a graph. All peptides having positive values with both algorithms and included in the first quadrant of the dot-scatter graph (double positive quadrant (+/+)) were likely to be highly immunogenic epitopes. Those peptides were included in a list of potential peptides to screen. In the presence of homoschedasticity, we selected only peptides showing mean values greater than 1 (among those having both the mean value greater than 0 and the standard deviation value greater than 1). Nine out of the 250 peptides were thus chosen within the CMV pp65 and their immunogenicity analyzed by ex vivo stimulation of PBMC and measured at the transcriptional level using the production of IFN-γ mRNA. Four out of nine peptides stimulated PBMCs from all HLA-A*0201 restricted CMV-seropositive subjects tested (p values: peptide #5, 0.011032; peptide #7, 0.015225; peptide #8, 0.025221; and peptide #9, 0.007302). The intracellular IFN-γ protein production by ex vivo peptide stimulation ranged from 0.14 to 0.62% compared to 0.03% for non stimulated cells. Moreover, each of the four selected peptide, either alone or in pool, was able to reactivate in vitro a strong immune T cell memory response, as measured by cytokine protein release and target cell lysis. The identification of multiple HLA class I restricted epitopes will allow the simultaneous administration of peptides with the ability to produce CMV-specific CTLs in patients bearing the same HLA types. This represents an extraordinary advantage for CMV adoptive immune therapy or vaccination.
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Zhang, Dingwa, Deyong He, Xiaoliang Pan, and Lijun Liu. "Rational Design and Intramolecular Cyclization of Hotspot Peptide Segments at YAP–TEAD4 Complex Interface." Protein & Peptide Letters 27, no. 10 (November 2, 2020): 999–1006. http://dx.doi.org/10.2174/0929866527666200414160723.
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Background: The Yes-Associated Protein (YAP) is a central regulator of Hippo pathway involved in carcinogenesis, which functions through interaction with TEA Domain (TEAD) transcription factors. Pharmacological disruption of YAP–TEAD4 complexes has been recognized as a potential therapeutic strategy against diverse cancers by suppressing the oncogenic activity of YAP. Objective: Two peptides, termed PS-1 and PS-2 are split from the interfacial context of YAP protein. Dynamics simulations, energetics analyses and fluorescence polarizations are employed to characterize the intrinsic disorder as well as binding energy/affinity of the two YAP peptides to TEAD4 protein. Methods: Two peptides, termed PS-1 and PS-2 are split from the interfacial context of YAP protein. Dynamics simulations, energetics analyses and fluorescence polarizations are employed to characterize the intrinsic disorder as well as binding energy/affinity of the two YAP peptides to TEAD4 protein. Result: The native conformation of PS-2 peptide is a cyclic loop, which is supposed to be constrained by adding a disulfide bond across the spatially vicinal residue pair Arg87-Phe96 or Met86- Phe95 at the peptide’s two ends, consequently resulting in two intramolecular cyclized counterparts of linear PS-2 peptide, namely PS-2(cyc87,96) and PS-2(cyc86,95). The linear PS-2 peptide is determined as a weak binder of TEAD4 (Kd = 190 μM), while the two cyclic PS-2(cyc87,96) and PS-2(cyc86,95) peptides are measured to have moderate or high affinity towards TEAD4 (Kd = 21 and 45 μM, respectively). Conclusion: PS-1 and PS-2 peptides are highly flexible and cannot maintain in native active conformation when splitting from the interfacial context, and thus would incur a considerable entropy penalty upon rebinding to the interface. Cyclization does not influence the direct interaction between PS-2 peptide and TEAD4 protein, but can largely reduce the intrinsic disorder of PS-2 peptide in free state and considerably minimize indirect entropy effect upon the peptide binding.
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Vitkova, Victoria, Krassimira Antonova, Ognyan Petkov, Angelina Stoyanova-Ivanova, Sirine Jaber, Vladislava Ivanova, Emilia Naydenova, and Dancho Danalev. "Interaction of KLAKLAK-NH2 and Analogs with Biomimetic Membrane Models." Pharmaceutics 16, no. 3 (February 28, 2024): 340. http://dx.doi.org/10.3390/pharmaceutics16030340.
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Background: Specifically designed peptide mimetics offer higher selectivity regarding their toxicity to mammalian cells. In addition to the α-helix conformation, the specific activity is related to the peptide’s ability to penetrate the cell membrane. The alterations in lipid membrane properties were addressed in the presence of the peptide KLAKLAK-NH2 and analogs containing β-alanine, strengthening the antibacterial activity and/or naphtalimide with proven anticancer properties. Methods: The molecular interactions of the peptide mimetics with POPC bilayers were studied using FTIR-ATR spectroscopy. The thermal shape fluctuation analysis of quasispherical unilamellar vesicles was applied to probe the membrane bending elasticity. The impedance characteristics of bilayer lipid membranes were measured using fast Fourier-transform electrochemical impedance spectroscopy. Results: A lateral peptide association with the membrane is reported for β-alanine-containing peptides. The most pronounced membrane softening is found for the NphtG-KLβAKLβAK-NH2 analog containing both active groups that corroborate with the indications for 1,8-naphthalimide penetration in the lipid hydrophobic area obtained from the FTIR-ATR spectra analysis. The β-alanine substitution induces strong membrane-rigidifying properties even at very low concentrations of both β-alanine-containing peptides. Conclusions: The reported results are expected to advance the progress in tailoring the pharmacokinetic properties of antimicrobial peptides with strengthened stability towards enzymatic degradation. The investigation of the nonspecific interactions of peptides with model lipid membranes is featured as a useful tool to assess the antitumor and antimicrobial potential of new peptide mimetics.
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Isaac, R. E., R. J. Siviter, P. Stancombe, D. Coates, and A. D. Shirras. "Conserved roles for peptidases in the processing of invertebrate neuropeptides." Biochemical Society Transactions 28, no. 4 (August 1, 2000): 460–64. http://dx.doi.org/10.1042/bst0280460.
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Invertebrates use a wide range of peptides as transmitters and hormones to regulate complex behaviour, physiology and development. These animals, especially those that are amenable to genetic study and are the subject of genome-sequencing projects, provide powerful model systems for understanding the functions of peptidases in controlling the bioactivity of peptides. Neprilysin, a zinc metallopeptidase and a key enzyme in the metabolism of mammalian peptides, is also implicated in the inactivation of peptides at synapses and of circulating peptide hormones in insects and nematodes. A family of neprilysin-like genes are present in the genomes of both Drosophila melanogaster and Caenorhabditis elegans; in C. elegans it seems that individual family members have evolved to take on different physiological functions, because they are expressed in a tissue-specific manner. Angiotensin I-converting enzymes (peptidyl dipeptidase A, angiotensin-converting enzyme) are another group of zinc metallopeptidases found in some invertebrates that lack angiotensin peptides. In D. melanogaster there are two functional angiotensin-converting enzymes that are essential for normal development. One of these (Acer) is expressed in the embryonic heart, whereas the second enzyme (Ance) is expressed in several tissues at different stages of the life cycle. The accumulation of Ance within secretory vesicles of some peptide-synthesizing cells suggests a role for the enzyme in the intracellular processing of insect peptides. Ance is very efficient at cleaving pairs of basic residues from the C-terminus of partly processed peptides, suggesting a novel role for the enzyme in prohormone processing. Invertebrates will continue to provide insights into the evolutionarily conserved functions of known peptidases and of those additional family members that are expected to be identified in the future from genome-sequencing projects.
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Schrul, Bianca, Katja Kapp, Irmgard Sinning, and Bernhard Dobberstein. "Signal peptide peptidase (SPP) assembles with substrates and misfolded membrane proteins into distinct oligomeric complexes." Biochemical Journal 427, no. 3 (April 14, 2010): 523–34. http://dx.doi.org/10.1042/bj20091005.
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SPP (signal peptide peptidase) is an aspartyl intramembrane cleaving protease, which processes a subset of signal peptides, and is linked to the quality control of ER (endoplasmic reticulum) membrane proteins. We analysed SPP interactions with signal peptides and other membrane proteins by co-immunoprecipitation assays. We found that SPP interacts specifically and tightly with a large range of newly synthesized membrane proteins, including signal peptides, preproteins and misfolded membrane proteins, but not with all co-expressed type II membrane proteins. Signal peptides are trapped by the catalytically inactive SPP mutant SPPD/A. Preproteins and misfolded membrane proteins interact with both SPP and the SPPD/A mutant, and are not substrates for SPP-mediated intramembrane proteolysis. Proteins interacting with SPP are found in distinct complexes of different sizes. A signal peptide is mainly trapped in a 200 kDa SPP complex, whereas a preprotein is predominantly found in a 600 kDa SPP complex. A misfolded membrane protein is detected in 200, 400 and 600 kDa SPP complexes. We conclude that SPP not only processes signal peptides, but also collects preproteins and misfolded membrane proteins that are destined for disposal.
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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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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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JACKSON, I. M. D. "Peptide Biology: Regulatory Peptides." Science 246, no. 4928 (October 20, 1989): 389–90. http://dx.doi.org/10.1126/science.246.4928.389-a.
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López-García, Belén, Luis González-Candelas, Enrique Pérez-Payá, and Jose F. Marcos. "Identification and Characterization of a Hexapeptide with Activity Against Phytopathogenic Fungi That Cause Postharvest Decay in Fruits." Molecular Plant-Microbe Interactions® 13, no. 8 (August 2000): 837–46. http://dx.doi.org/10.1094/mpmi.2000.13.8.837.
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A hexapeptide of amino acid sequence Ac-Arg-Lys-Thr-Trp-Phe-Trp-NH 2 was demonstrated to have antimicrobial activity against selected phytopathogenic fungi that cause postharvest decay in fruits. The peptide synthesized with either all D- or all L-amino acids inhibited the in vitro growth of strains of Penicillium italicum, P. digitatum, and Botrytis cinerea, with MICs of 60 to 80 μM and 50% inhibitory concentration (IC50) of 30 to 40 μM. The inhibitory activity of the peptide was both sequence- and fungus-specific since (i) sequence-related peptides lacked activity (including one with five residues identical to the active sequence), (ii) other filamentous fungi (including some that belong to the genus Penicillium) were insensitive to the peptide's antifungal action, and (iii) the peptide did not inhibit the growth of several yeast and bacterial strains assayed. Experiments on P. digitatum identified conidial germination as particularly sensitive to inhibition although mycelial growth was also affected. Our findings suggest that the inhibitory effect is initially driven by the electrostatic interaction of the peptide with fungal components. The antifungal peptide retarded the blue and green mold diseases of citrus fruits and the gray mold of tomato fruits under controlled inoculation conditions, thus providing evidence for the feasibility of using very short peptides in plant protection. This and previous studies with related peptides indicate some degree of peptide amino acid sequence and structure conservation associated with the antimicrobial activity, and suggest a general sequence layout for short antifungal peptides, consisting of one or two positively charged residues combined with aromatic amino acid residues.
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Iwasaki, Yu, Yuki Taga, Asahi Suzuki, Mihoko Kurokawa, Yoshio Sato, and Yasutaka Shigemura. "Effect of Co-Ingestion of Collagen Peptides with Yogurt on Blood Absorption of Short Chain Hydroxyproline Peptides." Applied Sciences 10, no. 12 (June 12, 2020): 4066. http://dx.doi.org/10.3390/app10124066.
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Collagen peptides (CP) have been used as functional foods for enhancing skin and joint health. Further degradation of CP results in peptide sizes small enough to enter the bloodstream following absorption in the small intestine. We examined the effects of food matrices on CP degradation into short chain peptides and absorption efficiency after ingestion. Changes to hydroxyproline (Hyp)-containing peptide levels in CP after yogurt fermentation and in human plasma by co-ingestion of CP and yogurt, with or without fermentation, were evaluated by liquid chromatography-mass spectrometry (LC-MS). The fermentation of CP with yogurt resulted in the significant degradation of CP into several Hyp-containing peptides such as Ala-Hyp, Leu-Hyp, Phe-Hyp, Ala-Hyp-Gly, and Leu-Hyp-Gly. CP ingestion after yogurt fermentation significantly increased the plasma concentrations of Phe-Hyp, cyclo(Ala-Hyp), and cyclo(Pro-Hyp) compared to water-based CP ingestion. The co-ingestion of CP and yogurt without fermentation significantly increased the plasma levels of Ala-Hyp, Phe-Hyp, Ala-Hyp-Gly, Leu-Hyp-Gly, Pro-Hyp-Gly, cyclo(Ala-Hyp), cyclo(Glu-Hyp), and cyclo(Pro-Hyp). Overall, the co-ingestion of CP and yogurt with or without fermentation significantly enhanced the absorption of CP-derived peptides, represented by the high Cmax and area under the curve per 1 h (AUC, nmol/h·mL) of Hyp-containing peptides. These results suggest that, in addition to increasing short chain Hyp-containing peptide levels via fermentation, yogurt matrices containing milk-derived peptides and/or lactic acid bacteria-derived peptidases may influence the efficient absorption of CP-derived peptides into human blood.
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Shevchenko, K. V., I. Yu Nagaev, L. A. Andreeva, V. P. Shevchenko, and N. F. Myasoedov. "Stability of prolin-containing peptides in biological media." Biomeditsinskaya Khimiya 65, no. 3 (2019): 180–201. http://dx.doi.org/10.18097/pbmc20196503180.
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New data on peptide drugs have been summarized; their high stability is due to both the introduction of Pro-Gly-Pro in various amino acid sequences and the modification of the glyproline fragment itself. Pro-Gly-Pro-Leu, ACTH(6-9)Pro-Gly-Pro, 5-oxo-Pro-Arg-Pro and 5-oxo-Pro-His-Pro-NH2 were used as proline-containing peptides. Tritiated peptides were obtained: Pro-Gly-Pro-Leu with specific radioactivity of 135 Ci/mmol, ACTH(6-9)Pro-Gly-Pro – 26 Ci/mmol, 5-oxo-Pro-Arg-Pro – 60 Ci/mmol and 5-oxo-Pro-His-Pro-NH2 – 75 Ci/mmol. The concentration of Pro-Gly-Pro-Leu, ACTH(6-9)Pro-Gly-Pro, 5-oxo-Pro-Arg-Pro and 5-oxo-Pro-His-Pro-NH2 in the blood was found to be about 200 times more than in the brain for intranasal administration, and in average 600 times more for intravenous administration. The stability of proline-containing peptides in vitro experiments was determined using different commercially available peptidases (leucine aminopeptidases, dipeptidases, carboxypeptidases B and Y), and using nasal mucus, microsomal fraction of the rat brain (IMPC) and rat blood plasma. During peptidase hydrolysis of Pro-Gly-Pro-Leu, the main metabolites were Gly-Pro-Leu, Pro-Gly-Pro, Gly-Pro and Pro-Gly. For ACTH(6-9)Pro-Gly-Pro, the main metabolites were Phe-Arg-Trp-Pro-Gly-Pro and Trp-Pro-Gly-Pro. In peptidase hydrolysis of 5-oxo-Pro-His-Pro-NH2, the major metabolite was 5-oxo-Pro-His-Pro. It was shown that with different methods of peptides administration the composition of the metabolites formed is different. Based on the data obtained, resistance to enzymatic cleavage of peptides and their metabolic pathways were evaluated. Thus, these new data have shown that the above approaches can be used to prolong the action of glyprolines in living objects. In this case, the degradation of proline-containing peptides occurs mainly not due to the action of proteases, but due to other ways of degradation. In general, the data presented in the review indicate the promise of intranasal way of introducing biologically active peptides into the brain of living organisms.
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Lu, Yating, Peng Lu, Yu Wang, Xiaodong Fang, Jianming Wu, and Xiaochang Wang. "A Novel Dipeptidyl Peptidase IV Inhibitory Tea Peptide Improves Pancreatic β-Cell Function and Reduces α-Cell Proliferation in Streptozotocin-Induced Diabetic Mice." International Journal of Molecular Sciences 20, no. 2 (January 14, 2019): 322. http://dx.doi.org/10.3390/ijms20020322.
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Dipeptidyl peptidase IV (DPP-IV) inhibitors occupy a growing place in the drugs used for the management of type 2 diabetes. Recently, food components, including food-derived bioactive peptides, have been suggested as sources of DPP-IV inhibitors without side effects. Chinese black tea is a traditional health beverage, and it was used for finding DPP-IV inhibitory peptides in this study. The ultra-filtrated fractions isolated from the aqueous extracts of black tea revealed DPP-IV inhibitory activity in vitro. Four peptides under 1 kDa were identified by SDS-PAGE and LC-MS/MS (Liquid Chromatography-Mass Spectrometry-Mass Spectrometry) from the ultra-filtrate. The peptide II (sequence: AGFAGDDAPR), with a molecular mass of 976 Da, showed the greatest DPP-IV inhibitory activity (in vitro) among the four peptides. After administration of peptide II (400 mg/day) for 57 days to streptozotocin (STZ)-induced hyperglycemic mice, the concentration of glucagon-like peptide-1 (GLP-1) in the blood increased from 9.85 ± 1.96 pmol/L to 19.22 ± 6.79 pmol/L, and the insulin level was increased 4.3-fold compared to that in STZ control mice. Immunohistochemistry revealed the improved function of pancreatic beta-cells and suppressed proliferation of pancreatic alpha-cells. This study provides new insight into the use of black tea as a potential resource of food-derived DPP-IV inhibitory peptides for the management of type 2 diabetes.
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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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Racheva, M., O. Romero, K. K. Julich-Gruner, A. S. Ulrich, C. Wischke, and A. Lendlein. "Purity of mushroom tyrosinase as a biocatalyst for biomaterial synthesis affects the stability of therapeutic peptides." MRS Proceedings 1718 (2015): 85–90. http://dx.doi.org/10.1557/opl.2015.260.
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ABSTRACTThe formation of injectable implants in the presence of cells or solutes has previously been conceptualized to be based on the selectivity of bioorthogonal chemical reactions. As an alternative approach, hydrogel network synthesis by enzymatic reactions with a typically high inherent substrate specificity and low toxicity have been repeatedly proposed, e.g. using commercial mushroom tyrosinase (MTyr), which specifically catalyzes phenol oxidation. In this study, it should be explored whether MTyr is compatible with therapeutic peptides that may be delivered from such hydrogels in the future. Based on the specificity of MTyr to phenol residues, no modification of peptides lacking the amino acid tyrosine would be expected. One example of such peptides is gramicidin S (GS), a potent antimicrobial peptide. However, when GS was incubated with commercial MTyr, peptide degradation occurred as observed by HPLC analysis. Several fragments of the peptide were detected by MALDI-TOF. Contamination of MTyr with peptidases was proven as the source of undesired peptide cleavage, which needs to be considered when preparing enzymatically crosslinked hydrogels for biomedical applications.
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Duncan, Ann-Maree, Athena Kladis, Garry L. Jennings, Anthony M. Dart, Murray Esler, and Duncan J. Campbell. "Kinins in humans." American Journal of Physiology-Regulatory, Integrative and Comparative Physiology 278, no. 4 (April 1, 2000): R897—R904. http://dx.doi.org/10.1152/ajpregu.2000.278.4.r897.
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The kinin peptide system in humans is complex. Whereas plasma kallikrein generates bradykinin peptides, glandular kallikrein generates kallidin peptides. Moreover, a proportion of kinin peptides is hydroxylated on proline3 of the bradykinin sequence. We established HPLC-based radioimmunoassays for nonhydroxylated and hydroxylated bradykinin and kallidin peptides and their metabolites in blood and urine. Both nonhydroxylated and hydroxylated bradykinin and kallidin peptides were identified in human blood and urine, although the levels in blood were often below the assay detection limit. Whereas kallidin peptides were more abundant than bradykinin peptides in urine, bradykinin peptides were more abundant in blood. Bradykinin and kallidin peptide levels were higher in venous than arterial blood. Angiotensin-converting enzyme inhibition increased blood levels of bradykinin, but not kallidin, peptides. Reactive hyperemia had no effect on antecubital venous levels of bradykinin or kallidin peptide levels. These studies demonstrate differential regulation of the bradykinin and kallidin peptide systems, and indicate that blood levels of bradykinin peptides are more responsive to angiotensin-converting enzyme inhibition than blood levels of kallidin peptides.
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Wojciechowska, Monika, Joanna Miszkiewicz, and Joanna Trylska. "Conformational Changes of Anoplin, W-MreB1–9, and (KFF)3K Peptides near the Membranes." International Journal of Molecular Sciences 21, no. 24 (December 18, 2020): 9672. http://dx.doi.org/10.3390/ijms21249672.
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Many peptides interact with biological membranes, but elucidating these interactions is challenging because cellular membranes are complex and peptides are structurally flexible. To contribute to understanding how the membrane-active peptides behave near the membranes, we investigated peptide structural changes in different lipid surroundings. We focused on two antimicrobial peptides, anoplin and W-MreB1–9, and one cell-penetrating peptide, (KFF)3K. Firstly, by using circular dichroism spectroscopy, we determined the secondary structures of these peptides when interacting with micelles, liposomes, E. coli lipopolysaccharides, and live E. coli bacteria. The peptides were disordered in the buffer, but anoplin and W-MreB1–9 displayed lipid-induced helicity. Yet, structural changes of the peptide depended on the composition and concentration of the membranes. Secondly, we quantified the destructive activity of peptides against liposomes by monitoring the release of a fluorescent dye (calcein) from the liposomes treated with peptides. We observed that only for anoplin and W-MreB1–9 calcein leakage from liposomes depended on the peptide concentration. Thirdly, bacterial growth inhibition assays showed that peptide conformational changes, evoked by the lipid environments, do not directly correlate with the antimicrobial activity of the peptides. However, understanding the relation between peptide structural properties, mechanisms of membrane disruption, and their biological activities can guide the design of membrane-active peptides.
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Krco, C. J., J. Pawelski, J. Harders, D. McCormick, M. Griffiths, H. S. Luthra, and C. S. David. "Characterization of the antigenic structure of human type II collagen." Journal of Immunology 156, no. 8 (April 15, 1996): 2761–68. http://dx.doi.org/10.4049/jimmunol.156.8.2761.
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Abstract A series of 101 peptides each 20 amino acids in length (10-residue overlap) spanning the helical portion of the mature alpha-chain of human type II collagen (CII) was synthesized. DBA/1 (H-2q) mice were immunized with individual peptides, and draining lymph node cells were challenged in vitro. Strong responses were measured to three peptides: peptide I (residues 74-93), peptide 14 (residues 254-273), and peptide 81 (residues 924-943). B10.Q (H-2q) mice were responsive to peptides I and 81 but not to peptide 14. B10.RIII (H-2r) mice, which are resistant to arthritis induction following immunization with human CII, were unresponsive to peptides I, 14, and 81. Using single amino acid truncated peptides, we determined minimal immunostimulatory lengths for peptides I and 81. Residues critical to antigenicity were identified by introducing alanine and glycine substitutions into minimal length immunostimulatory peptides. The determinants within peptides I and 81 are 100% homologous to mouse CII and are autoantigens. Peptide 81 has homology to viral proteins. Peptide 14 is 90% homologous to mouse CII and has homology to heat shock proteins.
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Tikhonov, S. L., N. V. Tikhonova, and E. A. Ulitina. "COMPARATIVE EVALUATION OF THE BIOLOGICAL EFFECT OF NATIVE AND SYNTHESIZED PEPTIDES." Vestnik of Immanuel Kant Baltic Federal University Series Natural and Medical Sciences, no. 3 (2023): 106–17. http://dx.doi.org/10.5922/gikbfu-2023-3-8.
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Biologically active peptides are considered as preventive and therapeutic agents for various diseases. Due to the high cost and complexity of isolating native peptides for use in pharmaceuticals, synthetically produced peptides are increasingly being used in dietary supplements. The aim of the research is to confirm the similarity and biological activity of synthesized peptides compared to native peptides. Synthesized and native peptides from bovine colostrum with the code names T1.1 and mpT2 were used as the objects of the study. The peptides were synthesized using the solid-phase method. Peptide T1.1 is similar to the peptide «POSSUM_01-POSSUM-C-EMBRYO-2KB», the biological activity of which has not been studied. Peptide mpT2 is similar to the anti-diabetic peptide «LL-16 Alytes obstetricans». It has been proven that the synthesized peptides do not differ from natural ones in terms of physical and chemical characteristics. Both synthesized and natural peptides are non-toxic. The anti-diabetic effect of natural and synthesized peptide mpT2 on animals with induced type 2 diabetes and the antioxidant activity of synthesized and natural peptide T1.1 have been demonstrated.
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Christensen, Jeffrey E., Jeffery R. Broadbent, and James L. Steele. "Hydrolysis of Casein-Derived Peptides αS1-Casein(f1-9) and β-Casein(f193-209) by Lactobacillus helveticus Peptidase Deletion Mutants Indicates the Presence of a Previously Undetected Endopeptidase." Applied and Environmental Microbiology 69, no. 2 (February 2003): 1283–86. http://dx.doi.org/10.1128/aem.69.2.1283-1286.2003.
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ABSTRACT Peptides derived from hydrolysis of αS1-casein(f1-9) [αS1-CN(f1-9)] and β-CN(f193-209) with cell extracts of Lactobacillus helveticus CNRZ32 and single-peptidase mutants (ΔpepC, ΔpepE, ΔpepN, ΔpepO, and ΔpepX) were isolated by using reverse-phase high-performance liquid chromatography and were characterized by mass spectrometry. The peptides identified suggest that there was activity of an endopeptidase, distinct from previously identified endopeptidases (PepE and PepO), with specificity for peptide bonds C terminal to Pro residues. Identification of hydrolysis products derived from a carboxyl-blocked form of β-CN(f193-209) confirmed that the peptides were derived from the activity of an endopeptidase.
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Gunasekera, Devi, James C. Zimring, and Kathleen P. Pratt. "A unique MHCII-binding register correlates with HLA-associated immunogenicity of the major K blood group antigen." Journal of Immunology 198, no. 1_Supplement (May 1, 2017): 146.23. http://dx.doi.org/10.4049/jimmunol.198.supp.146.23.
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Abstract Kell is a glycoprotein expressed on red blood cells (RBCs). Its K and k isoforms contain either Met (K antigen) or Thr (k antigen) at position 193. Development of anti-K antibodies following K-mismatched blood transfusions can destroy RBCs, while cross-placental transfer of anti-K antibodies can destroy RBC precursors, resulting in Hemolytic Disease of the Newborn. HLA-DR11, DR13 and DR15 are over-represented among K-immunized patient populations. The immunogenicity of overlapping 15-mer Kell peptides with M193 or T193 at every possible position was investigated by Stephen et al (Blood. 2012;119(23):5563-5574). Surprisingly, peptide W179-M193, with the polymorphic M193T site at the peptide’s C-terminus, was the most effective at stimulating CD4 T cells from K-immunized women. The present study utilized MHCII binding prediction algorithms and quantitative peptide-MHCII binding assays to determine the binding registers, anchor residues and affinities of wild-type, truncated, and sequence-modified Kell peptides. Predictions were generated using IEDB and Propred algorithms. Competitive peptide-MHCII binding assays utilized 13 recombinant HLA-DRB1 monomers, Kell peptides and high-affinity reference peptides. Interestingly, the assays identified a unique binding register (W179-S187) restricted to HLA-DR11 and DR15, in addition to the polymorphic site, suggesting stronger MHCII avidity may explain the increased disease susceptibility associated with these alleles.
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Mucha, Piotr, Emilia Sikorska, Piotr Rekowski, and Jarosław Ruczyński. "Interaction of Arginine-Rich Cell-Penetrating Peptides with an Artificial Neuronal Membrane." Cells 11, no. 10 (May 13, 2022): 1638. http://dx.doi.org/10.3390/cells11101638.
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Arginine-rich cell-penetrating peptides (RRCPPs) exhibit intrinsic neuroprotective effects on neurons injured by acute ischemic stroke. Conformational properties, interaction, and the ability to penetrate the neural membrane are critical for the neuroprotective effects of RRCCPs. In this study, we applied circular dichroism (CD) spectroscopy and coarse-grained molecular dynamics (CG MD) simulations to investigate the interactions of two RRCPPs, Tat(49–57)-NH2 (arginine-rich motif of Tat HIV-1 protein) and PTD4 (a less basic Ala-scan analog of the Tat peptide), with an artificial neuronal membrane (ANM). CD spectra showed that in an aqueous environment, such as phosphate-buffered saline, the peptides mostly adopted a random coil (PTD4) or a polyproline type II helical (Tat(49–57)-NH2) conformation. On the other hand, in the hydrophobic environment of the ANM liposomes, the peptides showed moderate conformational changes, especially around 200 nm, as indicated by CD curves. The changes induced by the liposomes were slightly more significant in the PTD4 peptide. However, the nature of the conformational changes could not be clearly defined. CG MD simulations showed that the peptides are quickly attracted to the neuronal lipid bilayer and bind preferentially to monosialotetrahexosylganglioside (DPG1) molecules. However, the peptides did not penetrate the membrane even at increasing concentrations. This suggests that the energy barrier required to break the strong peptide–lipid electrostatic interactions was not exceeded in the simulated models. The obtained results show a correlation between the potential of mean force parameter and a peptide’s cell membrane-penetrating ability and neuroprotective properties.
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Carmona, Adriana K., Maria Aparecida Juliano, and Luiz Juliano. "The use of Fluorescence Resonance Energy Transfer (FRET) peptidesfor measurement of clinically important proteolytic enzymes." Anais da Academia Brasileira de Ciências 81, no. 3 (September 2009): 381–92. http://dx.doi.org/10.1590/s0001-37652009000300005.
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Proteolytic enzymes have a fundamental role in many biological processes and are associated with multiple pathological conditions. Therefore, targeting these enzymes may be important for a better understanding of their function and development of therapeutic inhibitors. Fluorescence Resonance Energy Transfer (FRET) peptides are convenient tools for the study of peptidases specificity as they allow monitoring of the reaction on a continuous basis, providing a rapid method for the determination of enzymatic activity. Hydrolysis of a peptide bond between the donor/acceptor pair generates fluorescence that permits the measurement of the activity of nanomolar concentrations of the enzyme. The assays can be performed directly in a cuvette of the fluorimeter or adapted for determinations in a 96-well fluorescence plate reader. The synthesis of FRET peptides containing ortho-aminobenzoic acid (Abz) as fluorescent group and 2, 4-dinitrophenyl (Dnp) or N-(2, 4-dinitrophenyl)ethylenediamine (EDDnp) as quencher was optimized by our group and became an important line of research at the Department of Biophysics of the Federal University of São Paulo. Recently, Abz/Dnp FRET peptide libraries were developed allowing high-throughput screening of peptidases substrate specificity. This review presents the consolidation of our research activities undertaken between 1993 and 2008 on the synthesis of peptides and study of peptidases specificities.
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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.