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Parent Peptide (parent + peptide)
Selected AbstractsDevelopment of a potent and selective GPR7 (NPBW1) agonist: a systematic structure,activity study of neuropeptide BJOURNAL OF PEPTIDE SCIENCE, Issue 6 2007Maki Kanesaka Abstract Neuropeptide B (NPB) has been recently identified as an endogenous ligand for GPR7 (NPBW1) and GPR8 (NPBW2) and has been shown to possess a relatively high selectivity for GPR7. In order to identify useful experimental tools to address physiological roles of GPR7, we synthesized a series of NPB analogs based on modification of an unbrominated form of 23 amino acids with amidated C -terminal, Br(,)NPB-23-NH2. We confirmed that truncation of the N -terminal Trp residue resulted in almost complete loss of the binding affinity of NPB for GPR7 and GPR8, supporting the special importance of this residue for binding. Br(,)NPB-23-NH2 analogs in which each amino acid in positions 4, 5, 7, 8, 9, 10, 12 and 21 was replaced with alanine or glycine exhibited potent binding affinity comparable to the parent peptide. In contrast, replacement of Tyr11 with alanine reduced the binding affinity for both GPR7 and GPR8 four fold. Of particular interest, several NPB analogs in which the consecutive amino acids from Pro4 to Val13 were replaced with several units of 5-aminovaleric acid (Ava) linkers retained their potent affinity for GPR7. Furthermore, these Ava-substituted NPB analogs exhibited potent agonistic activities for GPR7 expressed in HEK293 cells. Among the Ava-substituted NPB analogs, analog 15 (Ava-5) and 17 (Ava-3) exhibited potency comparable to the parent peptide for GPR7 with significantly reduced activity for GPR8, resulting in high selectivity for GPR7. These highly potent and selective NPB analogs may be useful pharmacological tools to investigate the physiological and pharmacological roles of GPR7. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd. [source] Antigenicity of chimeric and cyclic synthetic peptides based on nonstructural proteins of GBV-C/HGVJOURNAL OF PEPTIDE SCIENCE, Issue 4 2006T. Pérez Abstract In this work, new putative epitopes located in nonstructural proteins of GBV-C/HGV were synthesized using solid-phase chemistry for their use in immunoassays. The antigens were obtained in linear, chimeric and cyclic forms with the main aim of improving the sensitivity of the enzyme immunoassays. Our results showed, on one hand, that the combination of different antigens seems to be necessary to ensure good sensitivity and more specificity and, on the other hand, that cyclic compounds show higher ability to recognize anti-GBV-C/HGV antibodies than its parent peptide. Furthermore, CD and FTIR have been used in conjunction to characterize the conformational changes therein with synthetic constructs that could explain their different antigenicity. Copyright © 2005 European Peptide Society and John Wiley & Sons, Ltd. [source] Oligopeptide-mediated helix stabilization of model peptides in aqueous solutionJOURNAL OF PEPTIDE SCIENCE, Issue 2 2003Yoshitaka Maeda Abstract Oligopeptide-mediated helix stabilization of peptides in hydrophobic solutions was previously found by NMR and CD spectroscopic studies. The oligopeptide included the hydrophobic amino acids found in its parent peptide and were interposed by relevant basic or acidic amino acids. The strength of the interactions depended on the amino acid sequences. However, no helix-stabilizing effect was seen for the peptides in phosphate buffer solution, because the peptides assumed a random-coil structure. In order to ascertain whether the helix-stabilizing effect of an oligopeptide on its parent peptide could operate in aqueous solution, model peptides EK17 (Ac-AEAAAAEAAAKAAAAKA-NH2) and IFM17 (Ac-AEAAAAEIFMKAAAAKA-NH2) that may assume an ,-helix in aqueous solutions were synthesized. Interactions were examined between various oligopeptides (EAAAK, KAAAE, EIFMK, KIFME, KIFMK and EYYEE) and EK17 or IFM17 in phosphate buffer and in 80% trifluoroethanol (TFE),20% H2O solutions by CD spectra. EAAAK had little effect on the secondary structures of EK17 in both buffer and TFE solutions, while KAAAE, which has the reverse amino acid sequence of EAAAK, had a marked helix-destabilizing effect on EK17 in TFE. EIFMK and KIFME were found to stabilize the ,-helical structure of EK17 in phosphate buffer solutions, whereas KIFMK and EYYEE destabilized the ,-helical structure of EK17. EIFMK and KIFME had no effect on IFM17, because unexpectedly, IFM17 had appreciable amounts of ,-sheet structure in buffer solution. It was concluded that in order for the helix-stabilizing effects to operate effectively, the following factors should be satisfied: (1) the model peptide, the ,-helical conformation of which is to be stabilized, should essentially assume an ,-helical structure by nature, and (2) the hydrophobicity of the side-chains of the oligopeptide should be high enough for the oligopeptide to perform stable specific side chain,side chain intermolecular hydrophobic interactions with the model peptide. Copyright © 2003 European Peptide Society and John Wiley & Sons, Ltd. [source] An enigmatic peptide ligation reaction: Protease-catalyzed oligomerization of a native protein segment in neat aqueous solutionPROTEIN SCIENCE, Issue 4 2000Sangaralingam Kumaran Abstract We report an enigmatic peptide ligation reaction catalyzed by Glu-specific Staphylococcus aureus V8 protease that occurs in neat aqueous solution around neutral pH utilizing a totally unprotected peptide substrate containing free ,-carboxyl and ,-amino groups. V8 protease catalyzed a chain of ligation steps between pH 6 and 8 at 4 °C, producing a gamut of covalent oligomers (dimer through octamer or higher) of a native protein segment TAAAKFE (S39) derived from ribonuclease A (RNAse A). Size-exclusion chromatography suggested the absence of strong interaction between the reacting peptides. The circular dichroism spectra of monomer through pentamer showed length-dependent enhancement of secondary structure in the oligomers, suggesting that protease-catalyzed ligation of a monomer to an oligomer resulted in a product that was more structured than its precursor. The relative conformational stability of the oligomers was reflected in their ability to resist proteolysis, indicating that the oligomerization reaction was facilitated as a consequence of the "conformational trapping" of the product. The ligation reaction proceeded in two phases,slow formation and accumulation of the dimer followed by a fast phase of oligomerization, implying that the conformational trap encountered in the oligomerization reaction was a two-step process. The Gly substitution at any position of the TAAAKFE sequence was deleterious, suggesting that the first step of the conformational trap, namely the dimerization reaction, that proceeded very slowly even with the parent peptide, was quite sensitive to amino acid sequence. In contrast, the oligomerization reaction of an Ala analog, AAAAKFE, occurred in much the same way as S39, albeit with faster rate, suggesting that Ala substitution stabilized the overall conformational trapping process. The results suggest the viability of the product-directed "conformational trap" as a mechanism to achieve peptide ligation of totally unprotected peptide fragments in neat aqueous solution. Further, the study projects the presence of considerable innate synthetic potential in V8 protease, baring rich possibilities of protein engineering of this enzyme to generate a "V8 peptide ligase." [source] Rapid and specific high-performance liquid chromatography for the in vitro quantification of d -Lys6,GnRH in a microemulsion-type formulation in the presence of peptide oxidation productsBIOMEDICAL CHROMATOGRAPHY, Issue 2 2010Alexandra P. Kafka Abstract A high-performance liquid chromatography (HPLC) method for assay of d -Lys6,GnRH contained in a microemulsion-type formulation is described. The peptide is extracted from the microemulsion matrix and quantified using a two-step gradient method. Separation from microemulsion compounds and potential peptide oxidation products was achieved on a Jupiter C18 column at 40°C, using a gradient of 10,35% CH3CN for peptide elution. The correlation of peak intensity measured at 220 nm and peptide concentration was linear over the range 2.5,60 µg/mL with a correlation coefficient of 0.9997 and a y -intercept not significantly different from zero (p > 0.05). Intraday and interday variability of the assay was less than 5% for multiple injections of samples containing 7.5, 30 and 60 µg/mL. The lower limit of quantitation was calculated to be 0.38 µg/mL, and the lower limit of detection was 0.13 µg/mL. The assay was applied to samples that were stressed under physiological conditions (37°C, pH 7.4) over 4 days. Three degradation peaks were well resolved from the parent peptide, demonstrating the selectivity of the assay. Off-line MALDI TOF mass spectrometry was applied to identify these degradation species as oxidation products of the peptide. Copyright © 2009 John Wiley & Sons, Ltd. [source] SAR by Oxime-Containing Peptide Libraries: Application to Tsg101 Ligand OptimizationCHEMBIOCHEM, Issue 12 2008Fa Liu Dr. Abstract HIV-1 viral assembly requires a direct interaction between a Pro-Thr-Ala-Pro ("PTAP") motif in the viral protein Gag-p6 and the cellular endosomal sorting factor Tsg101. In an effort to develop competitive inhibitors of this interaction, an SAR study was conducted based on the application of post solid-phase oxime formation involving the sequential insertion of aminooxy-containing residues within a nonamer parent peptide followed by reaction with libraries of aldehydes. Approximately 15,20-fold enhancement in binding affinity was achieved by this approach. [source] Research Letter: Retroinverso Mimetics of S PeptideCHEMICAL BIOLOGY & DRUG DESIGN, Issue 6 2007Jagdish Rai The S peptide from ribonuclease S was used as a model system to explore the relationship between the native peptide and its retroinverso (RI) analog. As probed by circular dichroism, the conformations of S peptide and retroinverso S peptide (RIS peptide) are each right-handed helical conformation. The helical propensity of retro S peptide is greater than S peptide, in trifluoroethanol (TFE). In 70% TFE, the S peptide possesses greater helicity at pH 4 than at pH 7, whereas RIS peptide possesses greater helicity at pH 7 than at pH 4. The RIS peptide does not mimic the S peptide in binding to S protein. Specifically, the RIS peptide does not mimic the S peptide to effect RNase activity with S protein and it also does not inhibit the RNase activity of S peptide with S protein. The biological mimicry between the S peptide and its RIS analog depends on the conformation and relatedness of both the side chain and backbone substructures. The backbones in the S peptide and its RIS analog are reverted with respect to each other; however, the side chain patterns are predicted to be similar. Importantly, if the molecular interactions of backbone atoms of the S peptide and its binding to S protein, then the RIS analog would be unlikely to mimic this parent peptide. [source] Engineering Metal Complexes of Chiral Pentaazacrowns as Privileged Reverse-turn ScaffoldsCHEMICAL BIOLOGY & DRUG DESIGN, Issue 2 2007Ye Che Reverse turns are common structural motifs and recognition sites in protein/protein interactions. The design of peptidomimetics is often based on replacing the amide backbone of peptides by a non-peptidic scaffold while retaining the biologic mode of action. This study evaluates the potential of metal complexes of chiral pentaazacrowns conceptually derived by reduction of cyclic pentapeptides as reverse-turn mimetics. The possible conformations of metal complexes of chiral pentaazacrown scaffolds have been probed by analysis of 28 crystal structures complexed with six different metals (Mn, Fe, Co, Ni, Cu, and Zn). The solvated structures as well as the impact of complexation with different metals/oxidation states have been examined with density functional theory (DFT) calculation as explicitly represented by interactions with a single water molecule. The results suggest that most reverse-turn motifs seen in proteins could be mimicked effectively with a subset of metal complexes of chiral pentaazacrown scaffolds with an RMSD of approximately 0.3 Å. Due to the relatively fixed orientation of the pendant chiral side groups in these metal complexes, one can potentially elicit information about the receptor-bound conformation of the parent peptide from their binding affinities. The presence of 20 H-atoms on the pentaazacrown ring that could be functionalized as well as the conformational perturbations available from complexation with different metals offer a desirable diversity to probe receptors for reverse-turn recognition. [source] HP(2,9)-magainin 2(1,12), a synthetic hybrid peptide, exerts its antifungal effect on Candida albicans by damaging the plasma membraneJOURNAL OF PEPTIDE SCIENCE, Issue 4 2004Yoonkyung Park Abstract In our previous study, HP(2,9)-MA(1,12), HP-MA for short, a hybrid peptide incorporating residues 2,9 of Helicobacter pylori ribosomal protein L1 (HP) and residues 1,12 of magainin 2 (MA) was shown to have strong antibacterial activity. In this study the antifungal activity of HP-MA was evaluated using various fungi, and it was shown that the activity was increased when compared with the parent peptides. In order to investigate the fungicidal mechanism(s) of HP-MA its action against fungal cell membranes was examined by the potassium-release test, which showed that HP-MA caused an increase in the amount of K+ released from the cells. Furthermore, HP-MA induced significant morphological changes. These facts suggested that the fungicidal effect of HP-MA involves damaging the fungal cell membranes. CD investigators suggested that the ,-helical structure of these peptides plays an important role in their antibiotic effect, but that ,-helicity is less directly correlated with the enhanced antibiotic activity of the hybrid. Copyright © 2003 European Peptide Society and John Wiley & Sons, Ltd. [source] Potent Opioid Peptide Agonists Containing 4,-[N -((4,-phenyl)-phenethyl)carboxamido]phenylalanine (Bcp) in Place of TyrCHEMICAL BIOLOGY & DRUG DESIGN, Issue 5 2008Grazyna Weltrowska Analogues of the opioid peptides H-Tyr-c[d -Cys-Gly-Phe(pNO2)- d -Cys]NH2 (non-selective), H-Tyr- d -Arg-Phe-Lys-NH2 (,-selective) and dynorphin A(1-11)-NH2 (,-selective) containing 4,-[N -((4,-phenyl)-phenethyl)carboxamido]phenylanine (Bcp) in place of Tyr1 were synthesized. All three Bcp1 -opioid peptides retained high , opioid receptor binding affinity, but showed very significant differences in the opioid receptor selectivity profiles as compared with the corresponding Tyr1 -containing parent peptides. The cyclic peptide H-Bcp-c[d -Cys-Gly-Phe(pNO2)- d -Cys]NH2 turned out to be an extraordinarily potent, ,-selective opioid agonist, whereas the Bcp1 -analogue of dynorphin A(1-11)-NH2 displayed partial agonism at the , receptor. The obtained results suggest that the large biphenylethyl substituent contained in these compounds may engage in a hydrophobic interaction with a receptor subsite and thereby may play a role in the ligand's ability to induce a specific receptor conformation or to bind to a distinct receptor conformation in a situation of conformational receptor heterogeneity. [source] | ||||||||||