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Model Peptides (model + peptide)
Kinds of Model Peptides Selected AbstractsHow Post-Translational Modifications Influence Amyloid Formation: A Systematic Study of Phosphorylation and Glycosylation in Model PeptidesCHEMISTRY - A EUROPEAN JOURNAL, Issue 26 2010Malgorzata Broncel Abstract A reciprocal relationship between phosphorylation and O-glycosylation has been reported for many cellular processes and human diseases. The accumulated evidence points to the significant role these post-translational modifications play in aggregation and fibril formation. Simplified peptide model systems provide a means for investigating the molecular changes associated with protein aggregation. In this study, by using an amyloid-forming model peptide, we show that phosphorylation and glycosylation can affect folding and aggregation kinetics differently. Incorporation of phosphoserines, regardless of their quantity and position, turned out to be most efficient in preventing amyloid formation, whereas O-glycosylation has a more subtle effect. The introduction of a single ,-galactose does not change the folding behavior of the model peptide, but does alter the aggregation kinetics in a site-specific manner. The presence of multiple galactose residues has an effect similar to that of phosphorylation. [source] Thermal Stability of Dehydrophenylalanine-Containing Model Peptides as Probed by Infrared Spectroscopy: a Case Study of an , -Helical and a 310 -Helical PeptideCHEMISTRY & BIODIVERSITY, Issue 3 2006Alka Gupta Abstract The temperature-dependent secondary-structural changes in the two known helical model peptides Boc-Val-,Phe-Ala-Leu-Gly-OMe (1; , -helical) and Boc-Leu-Phe-Ala-,Phe-Leu-OMe (2; 310 -helical), which both comprise a single dehydrophenylalanine (,Phe) residue, were investigated by means of FT-IR spectroscopy (peptide film on KBr). Both the first-order and the better-resolved second-order derivative IR spectra of 1 and 2 were analyzed. The ,(NH) (3240,3340,cm,1), the Amide-I (1600,1700,cm,1), and the Amide-II (1510,1580,cm,1) regions of 1 and 2 showed significant differences in thermal-denaturation experiments (22°,144°), with the 310 -helical peptide (2) being considerably more stable. This observation was rationalized by different patterns and strengths of intramolecular H-bonds, and was qualitatively related to the different geometries of the peptides. Also, a fair degree of residual secondary-structural elements were found even in the ,denatured' states above 104° (1) or 134° (2). [source] Model peptide-based system used for the investigation of metal ions binding to histidine-containing polypeptidesBIOPOLYMERS, Issue 6 2010Manuela Murariu Abstract The reaction of histidine-containing polypeptides with toxic and essential metals and the molecular mechanism of complexation has yet to be determined, particularly with respect to the conformational changes of the interacting macromolecules. Therefore, a system of oligopeptides containing histidine residues in various positions of Ala or Gly sequences has been designed and used in heavy metal comparatively binding experiments. The role of spacing residues (Gly and Ala repeats) in selecting the various conformations was investigated. The newly synthesized peptides and metal ion adducts have been characterized by Fourier transform infrared spectroscopy (FTIR) as well as electrospray ion trap mass spectrometry (ESI,MS) and circular dichroism (CD). The analysis of CD-spectra of the four peptides in water revealed that the secondary structure depends much on the position of each amino acid in the peptide backbone. Our peptides system reveals various binding mechanisms of metal ions to peptides depending on the position of histidine residue and the corresponding conformations of Ala or Gly sequences. Biological and medical consequences of conformational changes of metal-bound peptides are further discussed. Thus, the binding of heavy metals to four peptides may serve as a model system with respect to the conformational consequences of the metal addition on the amino acid repeats situated in prion protein. © 2010 Wiley Periodicals, Inc. Biopolymers 93:497,508, 2010. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] Identification and quantification of in vitro adduct formation between protein reactive xenobiotics and a lysine-containing model peptideENVIRONMENTAL TOXICOLOGY, Issue 1 2003Peter Reichardt Abstract Formation of in vitro adducts between different classes of xenobiotics and the lysine-containing peptide Lys-Tyr was monitored by high-performance liquid chromatography and electrospray ionization mass spectrometry. The molecular structures of the main resulting products could be sensitively analyzed by mass spectrometry (flow injection analysis), enabling the detection of characteristic binding formations. Aldehydes such as formaldehyde, acetaldehyde, and benzaldehyde were shown to form stable linkages to lysine amino groups via Schiff bases. Other electrophilic substances (e.g., toluene-2,4-diisocyanate, 2,4-dinitro-1-fluorobenzene, 2,4,6-trinitrobenzene sulfonic acid, dansyl chloride, and phthalic acid anhydride) also formed covalent adducts with lysine residues. The reactivity of the compounds was quantified by measuring the amount of peptide that remained unchanged after incubation for a certain period with the xenobiotic. Although reactivity levels within this group of aldehydes varied only to a small extent, as would be expected, extreme differences were seen among the structurally heterogeneous group of nonaldehyde xenobiotics. These results support the hypothesis that simple chemical reactions may lead to the adduction of nucleophilic macromolecules such as peptides or proteins. Such reactions, in particular, Schiff base formation of aldehydes, have previously been shown to be capable of specifically interfering with costimulatory signaling on T cells. Our results suggest that electrophilic xenobiotics of other classes may also inherit the capacity to exert similar effects. Forming covalent linkage to peptides may represent a possible molecular mechanism of electrophilic xenobiotics in vivo, yielding immunotoxic effects. The model utilized in this study is appropriate for monitoring the adduction of xenobiotics to basic peptides and for analyzing the resulting molecular structures. © 2003 Wiley Periodicals, Inc. Environ Toxicol 18: 29,36, 2003. [source] Capsosomes with Multilayered Subcompartments: Assembly and Loading with Hydrophobic CargoADVANCED FUNCTIONAL MATERIALS, Issue 1 2010Leticia Hosta-Rigau Abstract Therapeutic artificial cells or organelles are nanoengineered vehicles that are expected to substitute for missing or lost cellular function. The creation of capsosomes, polymer carrier capsules containing liposomal subcompartments, is a promising approach towards constructing such therapeutic devices using the layer-by-layer assembly method. Herein, the assembly of intact, nonaggregated capsosomes containing multiple liposome layers is reported. It is also further demonstrated that thiocoraline, a hydrophobic model peptide with antitumor activity, can be efficiently loaded into the membrane of the liposomal subcompartments of the capsosomes. Cell viability assays verify the activity of the trapped antitumor cargo. It is also shown that pristine capsosomes do not display inherent cytotoxic effects. The ability to tune the number of liposome layers and hence the drug loading in capsosomes as well as their noncytotoxicity provide new opportunities for the creation of therapeutic artificial cells and organelles. [source] pH dependent self assembly of ,-amyloid(10-35) and ,-amyloid(10-35)-PEG3000JOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 3-1 2000P. Thiyagarajan Small angle neutron and x-ray scattering (SANS/SAXS) studies were conducted on the structure of the aggregates formed from both the truncated model peptide ,-Amyloid(10-35) (A,10-35) and a block copolymer ,-Amyloid(10-35)-PEG3000 (A,10-35 -PEG) in D2O at pHs from 3.0 to 7.0. These studies indicate that A,10-35 aggregates into rod-like particles (fibril) and their radii are strongly dependent on the pH of the solution. The fibril-fibril association in A,10-35 solutions is less at pH < 5.6, but becomes larger at higher pH. A,10-35 -PEG also assembles into rod-like particles whose radius is larger by about 30 Å than that for A,10-35 fibril at pH 4.2, while it is about 23 Å larger at higher pH. Contrast matching SAXS/SANS experiments that eliminate the coherent scattering from PEG reveal that PEG moiety is located at the periphery of the fibril. Also the mass per unit length of the peptide portion is similar for both A,10-35 and A,10-35 fibrils at pH 5.6. The mass per unit length of the rods from SANS provides key information on the packing of A,10-35 peptides in the fibril. [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] A study of phase separation in peptide-loaded HPMC films using Tzero -modulated temperature DSC, atomic force microscopy, and scanning electron microscopyJOURNAL OF PHARMACEUTICAL SCIENCES, Issue 7 2004Samana Hussain Abstract Despite the widespread use of drug-loaded polymeric systems, there is still considerable uncertainty with regard to the nature of the distribution of the drug within the polymer matrix. The aim of this investigation was to develop thermal and microscopic techniques whereby the miscibility and spatial distribution of a model peptide, cyclosporin A (CyA), in hydroxypropyl methylcellulose (HPMC) films may be studied. The new technique of Tzero -modulated temperature differential scanning calorimetry (Tzero MTDSC), scanning electron microscopy (SEM), and pulse force mode atomic force microscopy (PFM-AFM) were used in conjunction to study films prepared using a solvent evaporation process, with a solvent extraction study performed to elucidate the nature of the observed phases. Tzero MTDSC studies showed glass transitions for both the HPMC and CycA, with the Tg for the HPMC and CycA seen for the mixed systems. SEM showed two spherical phases of differing electron density. PFM-AFM also showed spheres of differing adhesion that increased in size on addition of drug. Pixel intensity analysis indicated that the smaller spheres corresponded to CycA. Exposure of the films to dichloromethane, in which CycA is soluble but HPMC is not, resulted in the presence of voids that corresponded well to the spheres suggested to correspond to the drug. It was concluded that the system had undergone extensive or complete phase separation, and that the thermal and microscopic techniques outlined above are an effective means by which this issue may be studied. © 2004 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 93:1672,1681, 2004 [source] Thermosensitive gel formation of novel polypeptides containing a collagen-derived Pro-Hyp-Gly sequence and an elastin-derived Val-Pro-Gly-Val-Gly sequenceJOURNAL OF POLYMER SCIENCE (IN TWO SECTIONS), Issue 23 2005Yasushi Morihara Abstract A triple-helix-forming collagen model peptide, (prolyl- trans -4-hydroxyprolyl-glycyl)10 [(Pro-Hyp-Gly)10], and a thermosensitive elastin-derived pentapeptide, valyl-prolyl-glycyl-valyl-glycyl (Val-Pro-Gly-Val-Gly), were copolymerized in various mole ratios using 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide hydrochloride and 1-hydroxybenzotriazole in dimethyl sulfoxide at 20 °C. All of the obtained polypeptides have molecular weight higher than 103 and contain a triple-helical structure, and showed an inverse phase transition from transparent solution to turbid suspension in response to a rise in temperature. The lower critical solution temperature of the polypeptide solution decreased upon increasing the content of Val-Pro-Gly-Val-Gly. Furthermore, polypeptides containing 82,86 mol % of Val-Pro-Gly-Val-Gly in composition showed reversible gel formation, suggesting that (Pro-Hyp-Gly)10 acts as a hydrated unit and Val-Pro-Gly-Val-Gly acts as a thermosensitive crosslinking point. These biodegradable thermosensitive polypeptides may be useful for biomedical applications, including, as a scaffold for tissue regeneration. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 6048,6056, 2005 [source] Bioaffinity magnetic reactor for peptide digestion followed by analysis using bottom-up shotgun proteomics strategyJOURNAL OF SEPARATION SCIENCE, JSS, Issue 3 2008Lucie Korecká Abstract We report an efficient and streamlined way to improve the analysis and identification of peptides and proteins in complex mixtures of soluble proteins, cell lysates, etc. By using the shotgun proteomics methodology combined with bioaffinity purification we can remove or minimize the interference contamination of a complex tryptic digest and so avoid the time-consuming separation steps before the final MS analysis. We have proved that by means of enzymatic fragmentation (endoproteinases with Arg-C or/and Lys-C specificity) connected with the isolation of specific peptides we can obtain a simplified peptide mixture for easier identification of the entire protein. A new bioaffinity sorbent was developed for this purpose. Anhydrotrypsin (AHT), an inactive form of trypsin with an affinity for peptides with arginine (Arg) or lysine (Lys) at the C-terminus, was immobilized onto micro/nanoparticles with superparamagnetic properties (silica magnetite particles (SiMAG),Carboxyl, Chemicell, Germany). This AHT carrier with a determined binding capacity (26.8 nmol/mg of carrier) was tested with a model peptide, human neurotensin, and the resulting MS spectra confirmed the validity of this approach. [source] Tightly winding structure of sequential model peptide for repeated helical region in Samia cynthia ricini silk fibroin studied with solid-state NMRPROTEIN SCIENCE, Issue 4 2003Yasumoto Nakazawa Abstract There are many kinds of silks from silkworms and spiders with different structures and properties, and thus, silks are suitable to study the structure-property relationship of fibrous proteins. Silk fibroin from a wild silkworm, Samia cynthia ricini, mainly consists of the repeated similar sequences by about 100 times where there are alternative appearances of the polyalanine (Ala)12,13 region and the Gly-rich region. In this paper, a sequential model peptide, GGAGGGYGGDGG(A)12GGAGDGYGAG, which is a typical sequence of the silk fibroin, was synthesized, and the atomic-level conformations of Gly residues at the N- and C-terminal ends of the polyalanine region were determined as well as that of the central Ala residue using 13C 2D spin diffusion solid-state nuclear magnetic resonance (NMR) under off-magic angle spinning. In the model peptide with ,-helical conformation, the torsion angle of the central Ala residue, the 19th Ala, was determined to be (,, ,) = (,60°, ,50°), which was a typical ,-helical structure, but the torsion angles of two Gly residues, the 12th and 25th Gly residues, which are located at the N- and C-terminal ends of the polyalanine region, were determined to be (,,,) = (,70°, ,30°) and (,,,) = (,70°, ,20°), respectively. Thus, it was observed that the turns at both ends of polyalanine with ,-helix conformation in the model peptide are tightly wound. [source] Two crystal modifications of (Pro-Pro-Gly)4 -Hyp-Hyp-Gly-(Pro-Pro-Gly)4 reveal the puckering preference of Hyp(X) in the Hyp(X):Hyp(Y) and Hyp(X):Pro(Y) stacking pairs in collagen helicesACTA CRYSTALLOGRAPHICA SECTION D, Issue 1 2010Kenji Okuyama Two crystal modifications of a collagen model peptide, (Pro-Pro-Gly)4 -Hyp-Hyp-Gly-(Pro-Pro-Gly)4 [where Hyp is (4R,2S)- l -hydroxyproline], showed very similar unit-cell parameters and belonged to the same space group P21. Both crystals exhibited pseudo-merohedral twinning. The main difference was in their molecular-packing arrangements. One modification showed pseudo-hexagonal packing, while the other showed pseudo-tetragonal packing. Despite their different packing arrangements, no significant differences were observed in the hydration states of these modifications. The peptide in the pseudo-tetragonal crystal showed a cyclic fluctuation of helical twists with a period of 20,Å, while that in the pseudo-hexagonal crystal did not. In these modifications, the puckering conformations of four of the 12 Hyp residues at the X position of the Hyp(X)-Hyp(Y)-Gly sequence were in the opposite conformations to the previous hypothesis that Hyp(X) residues involved in Hyp(X):Hyp(Y) and Hyp(X):Pro(Y) stacking pairs prefer up-puckering and down-puckering conformations, respectively. Detailed investigation of the molecular interactions between Hyp(X) and adjacent molecules revealed that these opposite conformations appeared because the puckering conformation, which follows the hypothesis, is subject to steric hindrance from the adjacent molecule. [source] Determination of intermolecular distance for a model peptide of Bombyx mori silk fibroin, GAGAG, with rotational echo double resonanceBIOPOLYMERS, Issue 2 2002Tsunenori Kameda Abstract Rotational echo double resonance NMR spectroscopy is applied for the determination of the distance of intermolecular chains of pentapeptide, GAGAG (G: Gly, A: Ala), a model typical of the crystalline domain in Bombyx mori silk fibroin. 1:4 mixture of G[1- 13C]AGAG and GAG[15N]AG with antiparallel ,-sheet structure was used to determine the distance of intermolecular hydrogen bonding between adjacent molecules within pleated sheet and the 13C,15N interatomic distance was determined to be 4.3 Å. On the other hand, 1:4 mixture of GAG[1- 13C]AG and GAG[15N]AG gave information on the interpleated sheet arrangement. When we assumed the same distances between two interpleated sheets, the distance was calculated to be 5.3 Å and the angle 15N,13C,15N was 180°. © 2002 Wiley Periodicals, Inc. Biopolymers 64: 80,85, 2002 [source] Site-Specific Functionalization of Proteins by Organopalladium Reactions,CHEMBIOCHEM, Issue 2 2007Koichiro Kodama Abstract A new carbon,carbon bond has been regioselectively introduced into a target position (position 32 or 174) of the Ras protein by two types of organopalladium reactions (Mizoroki,Heck and Sonogashira reactions). Reaction conditions were screened by using a model peptide, and the stability of the Ras protein under the reaction conditions was examined by using the wild-type Ras protein. Finally, the iF,Ras proteins containing a 4-iodo- L -phenylalanine residue were subjected to organopalladium reactions with vinylated or propargylated biotin. Site-specific biotinylations of the Ras protein were confirmed by Western blot and LC-MS/MS. [source] How Post-Translational Modifications Influence Amyloid Formation: A Systematic Study of Phosphorylation and Glycosylation in Model PeptidesCHEMISTRY - A EUROPEAN JOURNAL, Issue 26 2010Malgorzata Broncel Abstract A reciprocal relationship between phosphorylation and O-glycosylation has been reported for many cellular processes and human diseases. The accumulated evidence points to the significant role these post-translational modifications play in aggregation and fibril formation. Simplified peptide model systems provide a means for investigating the molecular changes associated with protein aggregation. In this study, by using an amyloid-forming model peptide, we show that phosphorylation and glycosylation can affect folding and aggregation kinetics differently. Incorporation of phosphoserines, regardless of their quantity and position, turned out to be most efficient in preventing amyloid formation, whereas O-glycosylation has a more subtle effect. The introduction of a single ,-galactose does not change the folding behavior of the model peptide, but does alter the aggregation kinetics in a site-specific manner. The presence of multiple galactose residues has an effect similar to that of phosphorylation. [source] Adsorption of Insulin Peptide on Charged Single-Walled Carbon Nanotubes: Significant Role of Ordered Water MoleculesCHEMPHYSCHEM, Issue 8 2009Jia-Wei Shen Abstract Ordered hydration shells: The more ordered hydration shells outside the charged CNT surfaces prevent more compact adsorption of the peptide in the charged CNT systems (see picture), but peptide binding strengths on the charged CNT surfaces are stronger due to the electrostatic interaction. Studies of adsorption dynamics and stability for peptides/proteins on single-walled carbon nanotubes (SWNTs) are of great importance for a better understanding of the properties and nature of nanotube-based biosystems. Herein, the dynamics and mechanism of the adsorption of the insulin chain B peptide on different charged SWNTs are investigated by explicit solvent molecular dynamics simulations. The results show that all types of surfaces effectively attract the model peptide. Water molecules play a significant role in peptide adsorption on the surfaces of charged carbon nanotubes (CNTs). Compared to peptide adsorption on neutral CNT surfaces, the more ordered hydration shells outside the tube prevent more compact adsorption of the peptide in charged CNT systems. This shield effect leads to a smaller conformational change and van der Waals interaction between the peptide and surfaces, but peptide binding strengths on charged CNT surfaces are stronger than those on the neutral CNT surface due to the strong electrostatic interaction. The result of these simulations implies the possibility of improving the binding strength of peptides/proteins on CNT surfaces, as well as keeping the integrity of the peptide/protein conformation in peptide/protein,CNT complexes by charging the CNTs. [source] CuI -Catalyzed Azide,Alkyne Intramolecular i -to-(i+4) Side-Chain-to-Side-Chain Cyclization Promotes the Formation of Helix-Like Secondary StructuresEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 3 2010Mario Scrima Abstract A solid-phase assembly of model peptides derived from human parathyroid hormone-related protein (11,19) containing ,-azido- and ,-yl-,-amino acid residues in positions i and i+4 was cyclised in solution by an intramolecular CuI -catalyzed azide,alkyne 1,3-dipolar Huisgen cycloaddition. These series of heterodetic cyclo-nonapeptides varied in the size of the disubstituted 1,2,3-triazolyl-containing bridge, the location and the orientation of the 1,2,3-triazolyl moiety within the bridge. The 1,2,3-triazolyl moiety, presented at either 1,4- or 4,1-orientation, is flanked by side chains containing 1,4 CH2 groups that result in bridges comprised from 4,7 CH2 groups connecting residues 13 and 17. Comprehensive conformational analysis employing CD, NMR and molecular dynamics reveals the conformational propensities of these heterodetic cyclo-nonapeptides. Cyclo-nonapeptides containing either the 7 methylene bridge (VII and VIII) or the 4 methylene bridge (II) are unstructured in structure-promoting solvent. Cyclo-nonapeptide I in which the 1,4-disubstituted 1,2,3-triazolyl is flanked by 3 and 1 CH2 groups in proximity to the respective residues 13 and 17, is stabilized in a non-canonical structure. All the other heterodetic cyclo-nonapeptides (III,VI) in which the 1,2,3-triazolyl is flanked by a total of 5 or 6 CH2 groups nicely accommodate ,-helical structures and reproduce very closely the helical structure stabilized by the analogous cyclo-nonapeptide in which Lys13 and Asp17 are bridged by the isosteric lactam. These studies suggest that the bioorthogonal i -to-(i+4) side-chain-to-side-chain cyclization via the prototypic "click reaction" offers a new and powerful approach for generating stable helix mimetic structures. [source] Purification and characterization of cathepsin B-like cysteine protease from cotyledons of daikon radish, Raphanus sativusFEBS JOURNAL, Issue 21 2008Akihiko Tsuji Plant cathepsin B-like cysteine protease (CBCP) plays a role in disease resistance and in protein remobilization during germination. The ability of animal cathepsin B to function as a dipeptidyl carboxypeptidase has been attributed to the presence of a dihistidine (His110-His111) motif in the occluding loop, which represents a unique structure of cathepsin B. However, a dihistidine motif is not present in the predicted sequence of the occluding loop of plant CBCP, as determined from cDNA sequence analysis, and the loop is shorter. In an effort to investigate the enzymatic properties of plant CBCP, which possesses the unusual occluding loop, we have purified CBCP from the cotyledons of daikon radish (Raphanus sativus) by chromatography through Sephacryl S-200, DEAE,cellulose, hydroxyapatite and organomercurial,Sepharose. The molecular mass of the enzyme was estimated to be 28 kDa by SDS/PAGE under reducing conditions. The best synthetic substrate for CBCP was t -butyloxycarbonyl Leu-Arg-Arg-4-methylcoumaryl 7-amide, as is the case with human cathepsin B. However, the endopeptidase activity of CBCP towards glucagon and adrenocorticotropic hormone showed broad cleavage specificity. Human cathepsin B preferentially cleaves model peptides via its dipeptidyl carboxypeptidase activity, whereas daikon CBCP displays both endopeptidase and exopeptidase activities. In addition, CBCP was found to display carboxymonopeptidase activity against the substrate o -aminobenzoyl-Phe-Arg-Phe(4-NO2). Daikon CBCP is less sensitive (1/7000) to CA-074 than human cathepsin B. Expression analysis of CBCP at the protein and RNA levels indicated that daikon CBCP activity in cotyledons is regulated by post-transcriptional events during germination. [source] The periplasmic peptidyl prolyl cis,trans isomerases PpiD and SurA have partially overlapping substrate specificitiesFEBS JOURNAL, Issue 13 2008Krista H. Stymest One of the rate-limiting steps in protein folding has been shown to be the cis,trans isomerization of proline residues, catalysed by a range of peptidyl prolyl cis,trans isomerases (PPIases). In the periplasmic space of Escherichia coli and other Gram-negative bacteria, two PPIases, SurA and PpiD, have been identified, which show high sequence similarity to the catalytic domain of the small PPIase parvulin. This observation raises a question regarding the biological significance of two apparently similar enzymes present in the same cellular compartment: do they interact with different substrates or do they catalyse different reactions? The substrate-binding motif of PpiD has not been characterized so far, and no biochemical data were available on how this folding catalyst recognizes and interacts with substrates. To characterize the interaction between model peptides and the periplasmic PPIase PpiD from E. coli, we employed a chemical crosslinking strategy that has been used previously to elucidate the interaction of substrates with SurA. We found that PpiD interacted with a range of model peptides independently of whether they contained proline residues or not. We further demonstrate here that PpiD and SurA interact with similar model peptides, and therefore must have partially overlapping substrate specificities. However, the binding motif of PpiD appears to be less specific than that of SurA, indicating that the two PPIases might interact with different substrates. We therefore propose that, although PpiD and SurA have partially overlapping substrate specificities, they fulfil different functions in the cell. [source] Cellular uptake of antisense oligonucleotides after complexing or conjugation with cell-penetrating model peptidesFEBS JOURNAL, Issue 16 2002J. Oehlke The uptake by mammalian cells of phosphorothioate oligonucleotides was compared with that of their respective complexes or conjugates with cationic, cell-penetrating model peptides of varying helix-forming propensity and amphipathicity. An HPLC-based protocol for the synthesis and purification of disulfide bridged conjugates in the 10,100 nmol range was developed. Confocal laser scanning microscopy (CLSM) in combination with gel-capillary electrophoresis and laser induced fluorescence detection (GCE-LIF) revealed cytoplasmic and nuclear accumulationin all cases. The uptake differences between naked oligonucleotides and their respective peptide complexes or conjugates were generally confined to one order of magnitude. No significant influence of the structural properties of the peptide components upon cellular uptake was found. Our results question the common belief that the increased biological activity of oligonucleotides after derivatization with membrane permeable peptides may be primarily due to improved membrane translocation. [source] Synthesis and Conformational Analysis of Pentapeptides Containing Enantiomerically Pure 2,2-Disubstituted GlycinesHELVETICA CHIMICA ACTA, Issue 3 2008Kathrin Abstract The synthesis and conformational analysis of model pentapeptides with the sequence Z-Leu-Aib-Xaa-Gln-Valol is described. These peptides contain two 2,2-disubstituted glycines (,,, -disubstituted , -amino acids), i.e., Aib (aminoisobutyric acid), and a series of unsymmetrically substituted, enantiomerically pure amino acids Xaa. These disubstituted amino acids were incorporated into the model peptides via the ,azirine/oxazolone method'. Conformational analysis was performed in solution by means of NMR techniques and, in the solid state, by X-ray crystallography. Both methods show that the backbones of these model peptides adopt helical conformations, as expected for 2,2-disubstitued glycine-containing peptides. [source] A comparison of quantum chemical models for calculating NMR shielding parameters in peptides: Mixed basis set and ONIOM methods combined with a complete basis set extrapolationJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 7 2006Seongho Moon Abstract This article compares several quantum mechanical approaches to the computation of chemical shielding tensors in peptide fragments. First, we describe the effects of basis set quality up to the complete basis set (CBS) limit and level of theory (HF, MP2, and DFT) for four different atoms in trans N -methylacetamide. For both isotropic shielding and shielding anisotropy, the MP2 results in the CBS limit show the best agreement with experiment. The HF values show quite a different tendency to MP2, and even in the CBS limit they are far from experiment for not only the isotropic shielding of carbonyl carbon but also most shielding anisotropies. In most cases, the DFT values differ systematically from MP2, and small basis-set (double- or triple-zeta) results are often fortuitously in better agreement with the experiment than the CBS ones. Second, we compare the mixed basis set and ONIOM methods, combined with CBS extrapolation, for chemical shielding calculations at a DFT level using various model peptides. From the results, it is shown that the mixed basis set method provides better results than ONIOM, compared to CBS calculations using the nonpartitioned full systems. The information studied here will be useful in guiding the selection of proper quantum chemical models, which are in a tradeoff between accuracy and cost, for shielding studies of peptides and proteins. © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 825,836, 2006 [source] Chemical cross-linking with NHS esters: a systematic study on amino acid reactivitiesJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 5 2009Stefanie Mädler Abstract Structure elucidation of tertiary or quaternary protein structures by chemical cross-linking and mass spectrometry (MS) has recently gained importance. To locate the cross-linker modification, dedicated software is applied to analyze the mass or tandem mass spectra (MS/MS). Such software requires information on target amino acids to limit the data analysis time. The most commonly used homobifunctional N-hydroxy succinimide (NHS) esters are often described as reactive exclusively towards primary amines, although side reactions with tyrosine and serine have been reported. Our goal was to systematically study the reactivity of NHS esters and derive some general rules for their attack of nucleophilic amino acid side chains in peptides. We therefore studied the cross-linking reactions of synthesized and commercial model peptides with disuccinimidyl suberate (DSS). The first reaction site in all cases was expectedly the ,-NH2 -group of the N -terminus or the ,-NH2 -group of lysine. As soon as additional cross-linkers were attached or loops were formed, other amino acids were also involved in the reaction. In addition to the primary amino groups, serine, threonine and tyrosine showed significant reactivity due to the effect of neighboring amino acids by intermediate or permanent Type-1 cross-link formation. The reactivity is highly dependent on the pH and on adjacent amino acids. Copyright © 2009 John Wiley & Sons, Ltd. [source] Effective detection of peptides containing cysteine sulfonic acid using matrix-assisted laser desorption/ionization and laser desorption/ionization on porous silicon mass spectrometryJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 1 2006Tomoya Kinumi Abstract Cysteine sulfonic acid-containing peptides, being typical acidic peptides, exhibit low response in matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. In this study, matrix conditions and the effect of diammonium hydrogencitrate (DAHC) as additive were investigated for ionization of cysteine sulfonic acid-containing peptides in MALDI. A matrix-free ionization method, desorption/ionization on porous silicon (DIOS), was also utilized to evaluate the effect of DAHC. When equimolar three-component mixtures of peptides carrying free cysteine, cysteine sulfonic acid, and carbamidomethyl cysteine were measured by MALDI using a common matrix, ,-cyano-4-hydroxycinnamic acid (CHCA), no signal corresponding to cysteine sulfonic acid-containing peptide could be observed in the mass spectrum. However, by addition of DAHC to CHCA, the peaks of cysteine sulfonic acid-containing peptides were successfully observed, as well as when using 2,4,6-trihydroxyacetophenone (THAP) and 2,6-dihydroxyacetophenone with DAHC. In the DIOS mass spectra of these analytes, the use of DAHC also enhanced the peak intensity of the cysteine sulfonic acid-containing peptides. On the basis of studies with these model peptides, tryptic digests of oxidized peroxiredoxin 6 were examined as a complex peptide mixture by MALDI and DIOS. In MALDI, the peaks of cysteine sulfonic acid-containing peptides were observed when using THAP/DAHC as the matrix, but this was not so with CHCA. In DIOS, the signal from cysteine sulfonic acid-containing peptides was suppressed; however, the use of DAHC significantly enhanced the signal intensity with an increase in the number of observed peptides and increased signal-to-noise ratio in the DIOS spectra. The results show that DAHC in the matrix or on the DIOS chip decreases discrimination and suppression effects in addition to suppressing alkali-adduct ions, which leads to a beneficial effect on protonation of peptides containing cysteine sulfonic acid. Copyright © 2005 John Wiley & Sons, Ltd. [source] Influence of "Alternative" C-terminal amino acids on the formation of [b3 + 17 + Cat]+ products from metal cationized synthetic tetrapeptides,JOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 5 2004V. Anbalagan Abstract The aim of this study was to investigate the dissociation patterns, and in particular the relative abundance of [b3 + 17 + Cat]+, for peptides with C-termini designed to allow transfer of the ,OH required to generate the product ion, but not necessarily as the most favored pathway. Working with the hypothesis that formation of a five-membered ring intermediate, including intramolecular nucleophilic attack by a carbonyl oxygen atom, is an important mechanistic step, several model peptides with general sequence AcFGGX were synthesized, metal cationized by electrospray ionization and subjected to collision-induced dissociation (CID). The amino acid at position X was one that either required a larger ring intermediate (,-alanine, ,-aminobutyric acid and ,-amino- n -caproic acid to generate six-, seven- or nine- membered rings, respectively) to transfer ,OH, lacked a structural element required for nucleophilic attack (aminoethanol) or prohibited cyclization because of the inclusion of a rigid ring (p - and m -aminobenzoic acid). For Ag+, Li+ and Na+ cationized peptides, our results show that amino acids requiring the adoption of larger ring intermediates suppressed the formation of [b3 + 17 + Cat]+, while amino acids that prohibit cyclization eliminated the reaction pathway completely. Formation of [b3 , 1 + Cat]+ from the alkali metal cationized versions was not a favorable process upon suppression or elimination of the [b3 + 17 + Cat]+ pathway: the loss of H2O to form [M , H2O + Cat]+ was instead the dominant dissociation reaction observed. Multiple-stage dissociation experiments suggest that [M , H2O + Cat]+ is not [b4 , 1 + Cat]+ arising from the loss of H2O from the C-terminus, but may instead be a species that forms via a mechanism involving the elimination of an oxygen atom from an amide group. Copyright © 2004 John Wiley & Sons, Ltd. [source] Studies on the cellular uptake of substance P and lysine-rich, KLA-derived model peptides,JOURNAL OF MOLECULAR RECOGNITION, Issue 1 2005Johannes Oehlke Abstract In the last decade many peptides have been shown to be internalized into various cell types by different, poorly characterized mechanisms. This review focuses on uptake studies with substance P (SP) aimed at unravelling the mechanism of peptide-induced mast cell degranulation, and on the characterization of the cellular uptake of designed KLA-derived model peptides. Studies on structure,activity relationships and receptor autoradiography failed to detect specific peptide receptors for the undecapeptide SP on mast cells. In view of these findings, a direct interaction of cationic peptides with heterotrimeric G proteins without the participation of a receptor has been proposed. Such a process would require insertion into and translocation of peptides across the plasma membrane. In order to clarify whether a transport of cationic peptides into rat peritoneal mast cells is possible, transport studies were performed by confocal laser scanning microscopy (CLSM) using fluorescence-labeled Arg3,Orn7 -SP and its D -amino acid analog, all- D -Arg3,Orn7 -SP, as well as by electron microscopic autoradiography using 3H-labelled SP and 125I-labelled all- D -SP. The results obtained by CLSM directly showed translocation of SP peptides into pertussis toxin-treated cells. Kinetic experiments indicated that the translocation process was rapid, occurring within a few seconds. Mast cell degranulation induced by analog of magainin 2 amide, neuropeptide Y and the model peptide acetyl-KLALKLALKALKAALKLA-amide was also found to be very fast, pointing to an extensive translocation of the peptides. In order to learn more about structural requirements for the cellular uptake of peptides, the translocation behavior of a set of systematically modified KLA-based model peptides has been studied in detail. By two different protocols for determining the amount of internalized peptide, evidence was found that the structure of the peptides only marginally affects their uptake, whereas the efflux of cationic, amphipathic peptides is strikingly diminished, thus allowing their enrichment within the cells. Although the mechanism of cellular uptake, consisting of energy-dependent and -independent contributions, is not well understood, KLA-derived peptides have been shown to deliver various cargos (PNAs, peptides) into cells. The results obtained with SP- and KLA-derived peptides are discussed in the context of the current literature. Copyright © 2004 John Wiley & Sons, Ltd. [source] Synthesis of pathological and nonpathological human exon 1 huntingtinJOURNAL OF PEPTIDE SCIENCE, Issue 7 2010David Singer Abstract Huntington's disease (HD) is a neurodegenerative disorder that affects approximately 1 in 10 000 individuals. The underlying gene mutation was identified as a CAG-triplet repeat expansion in the gene huntingtin. The CAG sequence codes for glutamine, and in HD, an expansion of the polyglutamine (poly-Q) stretch above 35 glutamine residues results in pathogenicity. It has been demonstrated in various animal models that only the expression of exon 1 huntingtin, a 67-amino acid-long polypeptide plus a variable poly-Q stretch, is sufficient to cause full HD-like pathology. Therefore, a deeper understanding of exon 1 huntingtin, its structure, aggregation mechanism and interaction with other proteins is crucial for a better understanding of the disease. Here, we describe the synthesis of a 109-amino acid-long exon 1 huntingtin peptide including a poly-Q stretch of 42 glutamines. This microwave-assisted solid phase peptide synthesis resulted in milligram amounts of peptide with high purity. We also synthesized a nonpathogenic version of exon 1 huntingtin (90-amino acid long including a poly-Q stretch of 23 glutamine residues) using the same strategy. In circular dichroism spectroscopy, both polypeptides showed weak alpha-helical properties with the longer peptide showing a higher helical degree. These model peptides have great potential for further biomedical analyses, e.g. for large-scale pre-screenings for aggregation inhibitors, further structural analyses as well as protein,protein interaction studies. Copyright © 2010 European Peptide Society and John Wiley & Sons, Ltd. [source] Role of side chains in collagen triple helix stabilization and partner recognition,JOURNAL OF PEPTIDE SCIENCE, Issue 3 2009Rita Berisio Abstract Collagen is a widespread protein family involved in a variety of biological processes. The complexity of collagen and its fibrous nature prevent detailed investigations on the full-length protein. Reductionist approaches conducted by dissecting the protein complexity through the use of model peptides have proved to be quite effective. There are, however, several issues regarding structure,stability relationships, aggregation in higher-order assemblies, and partner recognition that are still extensively investigated. In this review, we discuss the role that side chains play in triple helix stabilization and in partner recognition. On the basis of recent literature data, we show that collagen triple helix stability is the result of the interplay of different factors. As a general trend, interactions established by amino/imino acid side chains within the triple helix scaffold effectively modulate the intrinsic residue propensity for this common structural motif. The use of peptide models has also highlighted the role that side chains play in collagen self-association and in its interactions with receptors. Valuable examples in these fields are illustrated. Finally, future actions required to obtain more detailed information on the structure and the function of this complex protein are also delineated. Copyright © 2008 European Peptide Society and John Wiley & Sons, Ltd. [source] Transition metal complexes of a cyclic pseudo hexapeptide: synthesis, complex formation and catalytic activities,,JOURNAL OF PEPTIDE SCIENCE, Issue 9 2008Huong Ngyen Abstract To contribute to a better understanding of metalloenzymes, we studied ion selectivity, complex formation tendencies and catalytic activities of linear and cyclic pseudopeptides. In this contribution, a linear and cyclic pseudo hexapeptide is described. The complex with transition metal ions and the sequence were designed using the programme COSMOS. Different routes of solid-phase synthesis were performed and compared using anchoring by C -terminus or a His side chain, using preformed pseudodipeptide building units or formation of N -functionalized peptide bond during stepwise assembly. The different strategies were compared regarding cyclization tendency, yield and purity. Side-chain anchoring to solid support favours the cyclization but leads to the formation of difficult to separate dioxopiperazine. Both routes require preformed building units. Complex-formation tendencies and selectivity for certain bivalent transition metal ions were experimentally estimated and compared to ones predicted theoretically. CD measurements indicate conformational changes by complex formation with different metal ions. Catalytic activities on oxidation of catechol and hydrolysis of bis-phosphate esters by some metal complexes of linear and cyclic peptide show only low catalytic activities compared to other model peptides and related metalloenzymes. The preference of the cyclic peptide for complexation of Ni2+ corresponds well to the predictions of COSMOS-NMR force field calculations. Copyright © 2008 European Peptide Society and John Wiley & Sons, Ltd. [source] Collagen-like triple helix formation of synthetic (Pro-Pro-Gly)10 analogues: (4(S)-hydroxyprolyl-4(R)-hydroxyprolyl-Gly)10, (4(R)-hydroxyprolyl-4(R)-hydroxyprolyl-Gly)10 and (4(S)-fluoroprolyl-4(R)-fluoroprolyl-Gly)10JOURNAL OF PEPTIDE SCIENCE, Issue 10 2005Masamitsu Doi Abstract For the rational design of a stable collagen triple helix according to the conventional rule that the pyrrolidine puckerings of Pro, 4-hydroxyproline (Hyp) and 4-fluoroproline (fPro) should be down at the X-position and up at the Y-position in the X-Y-Gly repeated sequence for enhancing the triple helix propensities of collagen model peptides, a series of peptides were prepared in which X- and Y-positions were altogether occupied by HypR, HypS, fProR or fProS. Contrary to our presumption that inducing the X-Y residues to adopt a down-up conformation would result in an increase in the thermal stability of peptides, the triple helices of (HypS -HypR -Gly)10 and (fProS -fProR -Gly)10 were less stable than those of (Pro-HypR -Gly)10 and (Pro-fProR -Gly)10, respectively. As reported by Bächinger's and Zagari's groups, (HypR -HypR -Gly)10 which could have an up-up conformation unfavorable for the triple helix, formed a triple helix that has a high thermal stability close to that of (Pro-HypR -Gly)10. These results clearly show that the empirical rule based on the conformational preference of pyrrolidine ring at each of X and Y residues should not be regarded as still valid, at least for predicting the stability of collagen models in which both X and Y residues have electronegative groups at the 4-position. Copyright © 2005 European Peptide Society and John Wiley & Sons, Ltd. [source] | |||||||||||||||||||||||||||||||||||||