bluuebunny/crossref_metadata_2025 huggingface dataset:
A rational approach for the development of reduced‐size analogues of neuropeptide Y with high affinity to the Y1 receptor
Authors: Rist Beate , Wieland Heike A. , Willim Klaus‐Dieter , Beck‐Sickinger Annette G.
Published: May 2005

Four sets of centrally truncated analogues of neuropeptide Y have been synthesized. In each series the N‐terminal part was constant, while the C‐terminal segment was systematically varied in length. The C‐ and N‐terminal parts were linked by 6‐aminohexanoic acid. The affinity to the Y1 receptor was investigated on human neuroblastoma cells SK‐N‐MC. Significant differences were found between the series of peptides as well as within each set. Remarkably, the affinity did not solely depend on the length of the segment, and with increasing numbers of residues the IC50 values were not always decreased. With a given N‐terminal segment, only one optimal length of the C‐terminal segment was found, which suggests that it is not the amino acids themselves but their 3D arrangement and orientation that is important for high receptor affinity.
Sweet and bitter taste: Structure and conformations of two aspartame dipeptide analogues
Authors: Benedetti Ettore , Gavuzzo Enrico , Santini Antonello , Kent Darin R. , Zhu Yun‐Fei , Zhu Qin , Mahr Christian , Goodman Murray
Published: May 2005

The synthesis and X‐ray diffraction analysis of two dipeptide taste ligands have been carried out as part of our study of the molecular basis of taste. The compounds L‐aspartyl‐D‐α‐methylphenylalanine methyl ester [L‐Asp‐D‐(αMe)Phe‐OMe] and L‐aspartyl‐D‐alanyl‐2,2,5,5‐tetramethylcyclopentanyl ester [L‐Asp‐D‐Ala‐OTMCP] elicit bitter and sweet taste, respectively. The C‐terminal residues of the two analogues adopt distinctly different conformations in the solid state. The aspartyl moiety assumes the same conformation found in other dipeptide taste ligands with the side‐chain carboxylate and the amino groups formaing a zwitterionic ring with a conformation defined by ψ,χX1 = 157.7°, −61.5° for L‐Asp‐D‐Ala‐OTMCP and 151.0°, −68.8° for L‐Asp‐D‐(αMe)Phe‐OMe. In the second residue, a left‐handed helical conformations is observed for the (αMe)Phe residue of L‐Asp‐D‐(αMe)Phe‐OMe with ϕ2 = 49.0° and ψ2 = 47.9°, while the Ala residue of L‐Asp‐D‐Ala‐OTMCP adopts a semi‐exextended conformation characterized by dihedral angles ϕ2 = 62.8° and ψ2 = −139.9°. The solid‐state structure of the bitter L‐Asp‐D‐(αMe)Phe‐OMe is extended; while the crystal structure of the sweet L‐Asp‐D‐OTMCP roughly adopts the typical L‐shaped structure shown by other sweeteners. The data of L‐Asp‐D‐(αMe)Phe‐OMe are compared with those of its diastereoisomer L‐Asp‐L‐(αMe)Phe‐OMe. Conformational analysis of the two taste ligands in solution by NMR and computer simulations agrees well with our model for sweet and bitter tastes.
Metal ion binding affinities of gastrin and CCK in membrane mimetic environments
Authors: Lutz Jürgen , Weyher Elisabeth , Moroder Luis
Published: May 2005

The fully active gastrin and CCK analogues [Nle15]‐gastrin‐ 17 and [Nle, Thr]‐CCK‐9 were analysed for their Ca2+ and Tb3+ affinities in various membrane mimetic conditions. In TFE both gastrin and CCK exhibited high affinities for calcium and terbium. At saturation level identical metal ion/peptide ratios were determined with Ca2+ and Tb3+, i.e. R = 3 for gastrin and R = 1 for CCK, confirming the very similar coordination properties of the two metal ions. The conformational effects of both metal ions were found to be very similar with a disordering effect in the case of gastrin and a conformational transition to β‐turn type structure in the case of CCK. In order to mimic more properly physiological conditions, similar experiments were performed in the prsence of phospholipid bilayers. No interaction of the peptides with the bilayers was observed even in the presence of phospholipid bilayers. No interaction of the peptides with the bilayers was observed even in the presence of mmolar Ca2+ concentrations. Induced lipid interaction via N‐terminal lipodervatization of gastrin and CCK allowed to translocate quantitatively the two hormones into phospholipid bilayers and to examine the effect of extravesicular Ca2+ on the conformation of the peptide headgroups and on their display at the water/lipid interphase. The CCK moiety of the lipo‐CCK inserted into phospholipid bilayers interacts with the lipid phase and addition of Ca2+ enhances the clustering of the peptide headgroups in a more β‐sheet type conformation. Conversely, insertion of lipo‐gastrin into the bilayers leads to full exposure of the gastrin headgroup to the bulk water in predominantly random coil structure. Again Ca2+ provokes aggregation. As the lipo‐peptide/phospholipid system still represents only an artificial model, it remains hazardous to derive a biological relevance from these data. The significantly higher affinity of lanthanide ions than Ca2+ for the peptides could well play a role in the inhibibitory activity of lanthanum on the signal transduction of the CCK family of hormones.
Use of a gel‐forming dipeptide derivative as a carrier for antigen presentation
Authors: Vegners Rolands , Shestakova Irina , Kalvinsh Ivars , Ezzell Robert M. , Janmey Paul A.
Published: May 2005

A dipeptide of the formula Fmoc‐Leu‐Asp and some other related dipeptides were synthesized in solution by standard methods. When such peptides are dissolved in water at concentrations below 1% at 100 °C and cooled below 60 °C they form turbid solutions and eventaully visocelastic gels at lower temperatures. Such gels are thermoreversible and can also be disrupted by mechanical agitation. At a concentration of 2 mg/ml the peptide Fmoc‐Leu‐Asp forms an aqueous gel at 60 °C with a shear modulus of 80 Pa measured at a frequency of 1 rad/s. Peptide solutions undergo an abrupt increase in light scattering between 1 and 1.5 mg/ml at both 23 and 60 °C. By analogy with previous observations of other systems, this increse appears to be due to the formation of filamentous micelles and the aggregation of filamaents into a three‐dimensional network. When low molecular weight adamantanamine derivatives, which are inherently non‐antigenci antiviral drugs, were incorporated into the Fmoc‐Leu‐Asp gel and injected into rabbits, high titre specific antibodies were efficiently produced without the need for additional adjuvant. Both the physical properties of the gel and its effect on the antigenicity of low molecular weight compounds suggest a number of practical applications.
Synthesis and biological characterization of a series of analogues of ω‐conotoxin gvia
Authors: Flinn James P. , Murphy Roger , Boubliek Jaroslav H. , Lew Michael J. , Writh Christine E. , Angus James A.
Published: May 2005

The 27‐residue polypeptide ω‐conotoxin GVIA (ω‐CgTx), from the venom of the cone shell Conus geographus, blocks N‐type neuronal calcium channels. It contains three disulphide bridges. We reporte here the synthesis and biological characterization of a seires of analogues in which one disulphide has been replaced by substitution of appropriate Cys residues with Ser, viz. [Ser1,16]‐ω‐CgTx, [Ser8,19]‐ω‐CgTx, [Ser15,26]‐ω‐CgTx, [Ser16]‐ω‐CgTx8‐27 and [Ser15]‐ω‐CgTx1‐19. All syntheses were conducted manually using either Boc or Fmoc methodology. Deprotected peptides were oxidized to their bridged forms using either aerial oxidation or aqueous dimethyl sulphoxide. Peptides were purified using RP‐HPLC, and their purity and identity were checked by RP‐HPLC, capillary electrophoresis and mass spectrometry. Inhibition of neuronal N‐type calcium channels was assessed as the inhibition of the twitch responses of rat vas deferens stimualted with single electrical pulses at 20 second intervals. None of these analogues was biologically active, suggesting that the disulphides play an important role in maintaining biological activity.
Application of the multiple antigenic peptides (MAP) strategy to the production of prophormone convertases antibodies: Synthesis, characterization and use of 8‐branched immunogenic peptides
Authors: Basak Ajoy , Boudreault Alain , Chen Andrew , Chrétien Michel , Seidah Nabil G. , Lazure Claude
Published: May 2005

Antiserum against an N‐terminal sequence of murine prohormone convertase‐1 (mPC1) incorporating the sequence immediatley following the junction between the putative pro‐region and the active enzyme was obtained. This was accomplished using the multiple antigenic peptide (MAP) approach whereupon an 8‐branched polylysine core to which are grafted multiple copies of a 16 amino acid peptide representing the N‐terminal sequence of mPC1 (positions 84–99) was synthesized by solid‐phase Fmoc chemistry. The ensuing peptide was purified and fully characterized by RP‐HPLC, 1H‐NMR, amino acid composition, peptide sequencing and ion‐spray mass spectrometry. The immunological properties of the resulting antibodies in detecting recombinant PC1 in both crude and purified preparations were compared with antibodies raised against a similar N‐terminal segment of PC1 but using the conventioanl method of peptide–carrier protein conjugation and also developed against a C‐terminal fusion protein of PC1. Our data indicate that the MAP antibody was as efficient as both the amino and carboxy‐terminal antibodies in qualitative as well as quantitative analysis of PC1 encoded protein by radioimmunoassay. Following an identical approach, antibodies against other prohormone convertases like furin, PC5/6 and PACE4 were also developed and subsequently applied to a number of biochemical and immunological studies. In each case, the ease of preparation and high immunogenicity of the MAP approach were confirmed and reside in the simplicity and rapidity with which a potent and useful antiserum is obtained.
Inversion of 310‐helix screw sense in a (D‐αMe)Leu homotetrapeptide induced by a guest D‐(αMe)val residue
Authors: Formaggio Fernando , Crisma Marco , Toniolo Claudio , Benedetti Ettore , Di Blasio Benedetto , Saviano Michele , Galdiero Stefania , Kamphuis John , Santini Antonello
Published: May 2005

The terminally blocked tetrapeptide pBrBz‐[D‐(αMe)Leu]2‐D‐(αMe)Val‐D‐(αMe)Leu‐OtBu is folded in the crystal state in a left‐handed 310‐helical structure stabilized by two consecutive 1 ← 4 CO ⃛HN intramolecular H‐bonds, as determined by X‐ray diffraction analysis. A CD study strongly supports the view that this conformation is also that largely prevailing in MeOH solution. A comparison with the published conformation of pBrBz‐[D‐(αMe)Leu]4‐OtBu indicates that incorporation of a single internal β‐branched (αMe)Val guest residue into the host homo‐tetrapeptide from the γ‐branched (αMe)Leu residue is responsible for a dramatic structural perturbation, i.e. an inversion of the 310 screw sense from right to left‐handed.
Inclusion volume solid‐phase synthesis
Authors: Eichler Jutta , Houghten Richard A. , Lebl Michal
Published: May 2005

Solid‐phase synthesis of peptides was carried out using only the volume of the solvent included in the swollen solid‐phase resin beads [inclusion volume synthesis]. This approach enables (i) the use of higher concentrations of activated amino acids, resulting in increased coupling rates, (ii) drastically decreased consumption of solvents, and (iii) the construction of multiple peptide synthesizers having virtually no reaction vessels.
Crystal Structure and Molecular Conformation of the Cyclic Hexapeptide cyclo‐(Gly‐Aib‐Gly)2
Authors: Escudero Encarnacion , Vidal Xavier , Solans Xavier , Peggion Evaristo , Subirana Juan Antonio
Published: May 2005

We have synthesized and crystallized the cyclic peptide (Gly‐Aib‐Gly) 2. Its structure has been determined by conventional X‐ray diffracti on methods. In the crystal it adopts a conformation with one β‐turn (type I) and its mirror image at the other side of the ring. All conformation al angles are similar to those reported for these amino acid residues. In particular the Aib residue has a conformation intermediate between α‐ and 310‐helical conformations. The ring is an adequate model for the β‐turn conformation. A molecule of formic acid is found in the crystal which shows a very short hydrogen bond with one of the glycine carbonyl groups.
The Solution Structure of the Immunodominant and Cell Receptor Binding Regions of Foot‐and‐mouth Disease Virus Serotype A, Variant A
Authors: Pegna M. , Molinari H. , Zetta L. , Gibbons W. A. , Brown F. , Rowlands D. , Siligardi G. , Mascagni P.
Published: May 2005

The solution structure of a 20 amino acid long peptide corresponding to the region 141–160 of the envelope protein Vp1 from foot‐and‐mouth disease virus (FMDV) serotype A, variant A, has been determined by a combination of NMR experiments and computer calculations. The peptide contains both the immunodominant epitope as well as the sequence (RGD) used by the virus to bind the cell receptor in the initial stages of infection. These two sites have been shown to partially overlap.

One hundred and thirty‐five NMR distance constraints were used to obtain a set of 11 structures by distance geometry, minimization and molecular dynamics simulations. These structures were divided into two homogeneous families based upon backbone superimposition. The first and most populated family was characterized by a backbone RMS of 1.5±0.4 Å, the second by a backbone RMS of 0.8±0.2 Å. The two families had similar structural features and differed mainly in the backbone angles of G149. In the larger of the two families these angles favoured the formation of a loop comprising residues 147 to 152 and stabilized by a H‐bond between the NH of D147 and the CO of A152. In the second family, where this bond was absent, the peptide adopted in this region the shape of an irregular helix. The C‐terminal half of the peptide (152–159) was similar in both families and largely helical. Similar structural features were also found within the VRGDS sequence (144–148) which was assigned to a β‐turn type IV. The features of the two families of structures were found to be different from those of the recently published X‐ray structure of the antigenic loop of a chemically modified form of FMDV. Proposals accounting for these differences are provided which take into account the dual activity of the 141–160 sequence (i.e. antibody binding and cell invasion through receptor binding).
The Solution Conformational Features of Two Highly Homologous Antigenic Peptides of Foot‐and‐mouth Disease Virus Serotype A, Variants A and USA, Correlate with their Serological Properties
Authors: Pegna M. , Molinari H. , Zetta L. , Melacini G. , Gibbons W. A. , Brown F. , Rowlands D. , Chan E. , Mascagni P.
Published: May 2005

The solution structure of a peptide corresponding to the VP1 region 141–160 of foot‐and‐mouth disease virus (FMDV) serotype A variant USA has been studied by NMR and computer calculations and compared with the results from a study on a highly homologous peptide deriving from serotype A, variant A. The two peptides differ in their serological behaviour and contain the immunodominant epitope of the virus which partly overlaps with its receptor binding region. Distance constraints, derived both from 2D and 3D homonuclear NMR and 2D‐heteronuclear NMR experiments, were combined with DG calculations to yield 50 structures. After refinement through EM and restrained molecular dynamics simulations the selected structures shared several general features. In particular the 151–158 region was a helix in all cases while a large loop similar to that found in peptide A but comprising less residues and stabilized by an H‐bond between the side chains of D147 and S150 was found in the majority of structures. A further loop, common to all structures, was identified around the RGD sequence (145–147). This was different from that found in the corresponding region of peptide A as were the conformations of the individual residues within the RGDX sequence.

The different structural features shown by the two peptides were rationalized in terms of the S148 (peptide A) to F148 (peptide USA) mutation. The second mutation, that at position 153 (L in A, P in USA) did not appear to affect the structure of the peptide significantly although the different dimensions of the loop in the central region and the type of H‐bond stabilizing it could be potentially ascribed to this second mutation.

All criteria used pointed to different structural features for the two peptides consistent with their serological behaviour.
Synthesis of a New Template with a Built‐in Adjuvant and Its Use in Constructing Peptide Vaccine Candidates Through Polyoxime Chemistry
Authors: Zeng Weiguang , Jackson David C. , Rose Keith
Published: May 2005

Synthetic lipopeptides are showing promise as vaccine candidates, but until now it has been very difficult to prepare them in homogeneous form. We describe the synthesis and characterization of a new water‐soluble, four‐branched template with a built‐in lipophilic adjuvant (Pam3Cys). Through the use of oxime chemistry, we attached four copies of an unprotected influenza virus peptide and characterized the product (13kDa) by reversed‐phase HPLC and electrospray ionization mass spectrometry. Several other such constructions were made using the new template and different peptides. We seem to have a general method for making synthetic lipopeptides in homogeneous form.
Effects of End Group and Aggregation on Helix Conformation: Crystal Structure of Ac‐(Aib‐Val‐Ala‐Leu)2‐Aib‐ OMe
Authors: Karle I. L. , Flippen‐Anderson J. L. , Uma K. , Balaram P.
Published: May 2005

The role of end groups in determining stereochemistry and packing in hydrophobic helical peptides has been investigated using an α‐aminosobutyric acid (Aib) containing model nonapeptide sequence. In contrast to the Boc‐analogue, Ac‐(Aib‐Val‐Ala‐Leu)2‐Aib‐OMe crystallizes with two independent molecules in a triclinic cell. The cell parameters are: space group P1, a=10.100(2)Å, b=15.194(4) Å, c=19.948(5) Å, α=63.12(2)°, β=88.03(2)°, γ=88.61(2)°, Z=2, R=7.96% for 5140 data where |Fo|>3σ(F). The two independent molecules alternate in infinite columns formed by head‐to‐tail hydrogen bonding. The helices in the two independent molecules are quite similar to each other but one molecule is rotated ≈︁123° about its helix axis with respect to the other. All the helical columns pack parallel to each other in the crystal. Replacement of the bulky Boc group does not lead to any major changes in conformation. Packing characteristics are also similar to those observed for similar helical peptides.
A Combinatorial Peptide Library Around Variation of the Human Immunode ficiency Virus (HIV‐1) V3 Domain Leads to Distinct T Helper Cell Responses
Authors: Estaquier Jérôme , Boutillon Christophe , Georges Bertrand , Ameisen Jean Claude , Tartar André , Auriault Claude
Published: May 2005

The hypervariable domain of the HIV gp120, the V3 loop domain, represents a target for neutralizing antibodies and for HIV vaccine strategies. In this study, we have investigated in murine species the potential cross‐reactivity of immune responses elicited by immunization either with individual V3 peptides, derived from distinct HIV sequences (BRU, RF, SF2, MN and ELI sequences), or with a V3 combinatorial peptide library.

We observed that individual V3 peptides are immunogenic but elicit a specific B‐ and T‐cell immune response that is mainly restricted to the sequence of the immunizing peptide. In particular, T‐cell responses that depend on T‐cell receptor recognition of peptides bound to the molecules encoded by the major histocompatibility complex were significantly influenced by small differences in the peptide amino acid sequence. The combinatorial V3 peptide library, previously described as B‐ and T‐cell immunogens, induced a more broadly reactive immune response, specially when T‐cell cytokine secretion was used as a readout for restimulation of T‐cells with individual V3 peptides.

These data suggest that amino acid variations in the sequence of an antigenic peptide could lead to the induction of different transducing signals in the primed T‐cell population and to the activation of T‐cells with distinct cytokine secretion properties. These observations may have implications in the understanding of antigenic variability and in the design of vaccine strategies.
The Importance of the Peptide Bond at Position 2 in HCO‐Met‐Leu‐Phe‐OMe Analogues as shown by Studies on Human Neutrophils
Authors: Cavicchioni Giorgio , Breveglieri Angela , Boggian Marisa , Vertuani Gianni , Reali Eva , Spisani Susanna
Published: May 2005

The formylpeptides formyl‐methionyl‐Nmethylleucyl‐ phenylaline methyl ester [for‐Met‐(NMe)Leu‐Phe‐OMe] 1, formyl‐methionyl‐2‐aminotetralin‐2‐carboxyl‐phenylalanine methyl ester [for‐Met Act‐Phe‐OMe] 2, formyl‐methionyl‐1,2,3,4‐terahydroisoquinoline‐3‐carboxl‐ phenylalanine methyl ester [for‐Met‐Tic‐Phe‐OMe] 3 and formyl‐ methionyl‐2‐aminoxy‐4‐methylvaleryl‐phenylalanine methyl ester [for‐Met‐OLeu‐Phe‐OMe] 4 were synthesized in order to investigate the role of the amide bond at position 2 on biological activities on human neutrophils. Only analogue 2, which keeps the NH group at position 2, was found to retain activity though sterically encumbered.
δ‐Selective Opioid Peptides Containing a Single Aromatic Residue in the Message Domain: An NMR Conformational Analysis
Authors: Crescenzi Orlando , Amodeo Pietro , Cavicchioni Giorgio , Guerrini Remo , Picone Delia , Salvadori Severo , Tancredi Teodorico , Temussi Piero A.
Published: May 2005

The sequence of deltorphin I, a δ‐selective opioid agonist, has been systematically modified by inserting conformationally constrained Cα,α disubstituted apolar residues in the third position. As expected, substitution of Phe with Ac6c, Ac5c and Ac3c yields analogues with decreasing but sizeable affinity. Surprisingly, substitution with Aib yields an analogue with almost the same binding affinity of the parent compound but with a greatly increased selectivity. This is the first case of a potent and very selective opioid peptide containing a single aromatic residue in the message domain, that is, only Tyr1. Here we report a detailed conformational analysis of [Aib3]deltorphin I and [Ac6c3]deltorphin I in DMSO at room temperature and in a DMSO/water cryomixture at low temperature, based on NMR spectroscopy and energy calculations. The peptides are highly structured in both solvents, as indicated by the exceptional finding of a nearly zero temperature coefficient of Val5 NH resonance. NMR data cannot be explained on the basis of a single structure but it was possible to interpret all NMR data on the basis of a few structural families. The conformational averaging was analysed by means of an original computer program that yields qualitative and quantitative composition of the mixture. Comparison of the preferred solution conformations with two rigid δ‐selective agonists shows that the shapes of [Aib3]deltorphin I and [Ac6c3]deltorphin I are consistent with those of rigid agonists and that the message domain of opioid peptides can be defined only in conformational terms.
Solid‐phase Synthesis and Cellular Localization of a C‐ and/or N‐terminal Labelled Peptide
Authors: Vidal P. , Chaloin L. , Méry J. , Lamb N. , Lautredou N. , Bennes R. , Heitz F.
Published: May 2005

We report the solid‐phase synthesis by the Fmoc strategy of a peptide containing a cysteamide group at its C‐terminus. This peptide was subject to further modifications including the linkage of fluorophores, namely lucifer yellow and coumarin respectively, at the C‐ and/or N‐terminals. After incubation with living cultured cells these two probes were localized and it is concluded that the post‐synthesis modifications can strongly modify the localization of the peptide.
Structural Polymorphism of Gramicidin A Channels: Ion Conductivity and Spectral Studies
Authors: Sychev Sergei V. , Sukhanov Stanislav V. , Barsukov Leonid I. , Ivanov Vadim T.
Published: May 2005

The relation between the various spatial structures of the gramicidin A channels and their ionic conductance has been studied. For this aim, various conformations of the peptide were pre‐formed in liposomal bilayer and after subsequent fusion of liposomes with planar lipid bilayer the measured channel conductance was correlated with gramicidin structures established in liposomes. To form the single‐stranded π6.3π 6.3 helix the peptide and lipid were co‐dissolved in TFE prior to liposome preparation. THF and other solvents were used to form parallel (↑ ↑ π π) and antiparallel (↑ ↓ π π) double helices. Conformation of gramicidin in liposomes made by various phosphatidylcholines was monitored by CD spectroscopy, and computer analysis of the spectra obtained was performed. After fusion of gramicidin containing liposomes with planar bilayer membranes from asolectin, the histograms of single‐channel conductance were obtained. The histograms had one or three distinct peaks depending on the liposome preparation. Assignment of the structure of the channel to conductance levels was made by correlation of CD data with conductance histograms. The channel‐forming analogue, des(Trp‐Leu)2‐gramicidin A, has been studied by the same protocol. The channel conductances of gramicidin A and the shortened analogue increase in the following order: ↑ ↓ π π 2 ↑ ↑ π π < π 6.3π6.3. Single‐channels formed by double helices have higher dispersity of conductance than the π6.3π6.3 helical channel. Lifetimes of the double helical and the π6.3π6.3 helical channels are very close to each other. The data obtained were compared with theoretically predicted properties of double helices [1].
The Structures of the Frenatin Peptides from the Skin Secretion of the Giant Tree Frog Litoria Infrafrenata
Authors: Raftery M. J. , Waugh R. J. , Bowie J. H. , Wallace J. C. , Tyler M. J.
Published: May 2005

The granular dorsal glands of the giant tree frog Litoria infrafrenata contain five peptides including caerulein (a known neuropeptide), and four new peptides named frenatins 1 (MH+ = 1140 Da), 2 (1423), 3 (2180) and 4 (2493). The amino acid sequences of the frenatins are detailed: their structures do not correspond to those of peptides isolated from other amphibians or animals. Frenatin 3, Gly‐Leu‐Met‐Ser‐Val‐Leu‐Gly‐His‐Ala‐Val‐Gly‐Asn‐Val‐Leu‐Gly‐ Gly‐Leu‐Phe‐Lys‐Pro‐Lys‐Ser‐(OH), has wide spectrum antimicrobial properties.
Synthesis of Fragments of the Peptide Component of Pseudobactin
Authors: Okonya John F. , Kolasa Teodozyj , Miller Marvin J.
Published: May 2005

Pseudobactin is a structurally complex and physiologically important siderophore (microbial iron chelator) from Pseudomonas putida‐ fluorescens. Various fragments of the unusual peptide component of pseudobactin listed below were prepared by solution‐phase peptide synthesis.

L‐Lys· D‐threo‐β‐OH Asp· L‐Ala· D‐allo‐Thr· L‐Ala

L‐Lys· D‐threo‐βOH Asp· L‐Ala· D‐allo‐Thr

D‐threo‐β‐OH Asp· L‐Ala· D‐ allo‐Thr· L‐Ala· D‐N‐OH‐cycloOrn

D‐threo‐β‐OH‐Asp· L‐Ala· D‐allo‐Thr· L‐Ala

L‐Ala· D‐allo‐Thr· L‐ Ala· D‐N‐OH‐cycloOrn

A class of related peptides named pseudomycins have shown promising antifungal activity. To examine if these peptide fragments above would elicit similar activity, the fragments were tested and found to have no antifungal activity in limited bioassays.
Conformational Analysis of Neuropeptide Y Segments by CD, NMR Spectroscopy and Restrained Molecular Dynamics
Authors: Gurrath Marion , Bisello Alessandro , Bottazzo Katia , Chung Chun‐Wa , Mammi Stefano , Peggion Evaristo
Published: May 2005

Neuropeptide Y (NPY), a peptide amide comprising 36 residue has been shown to act as a potent vasoconstrictor. In order to shed light on the structural requirements for the biological activities with respect to the different prerequisites for affinity to the NPY receptor subtypes Y1 and Y2, in the present study the syntheses and conformational analyses of two C‐terminal segments, NPY(18–36) and NPY(13–36), are described.

The results obtained by CD measurements, two‐dimensional NMR spectros copy and a conformational refinement of the NMR‐derived structure by molecular mechanics simulations support the findings of previously published structure –activity relationship studies for biologically active and selective compounds. In particular, the α‐helical conformation as well as an appropriate exposure of the side chains of the critical C‐terminal dipeptide within NPY(18–36) are in agreement with the prerequisites proposed for Y2 receptor binding of that segment.
Hydrophobic Effects on Antibacterial and Channel‐forming Properties of Cecropin A–Melittin Hybrids
Authors: Juvvadi Padmaja , Vunnam Satyanarayana , Merrifield Elizabeth L. , Boman Hans G. , Merrifield R. B.
Published: May 2005

The design of cecropin–melittin hybrid analogues is of interest due to the similarities in the structure of the antimicrobial peptides cecropin and melittin but differences in their lytic properties. We suspected that a hydrophobic residue in position 2 of milittin (Ile8 in the hybrid) plays an important role in the activity of the 15‐residue hybrid, KWKLFKKIGAVLKVL‐NH2, [CA(1–7)M(2–9)NH2] and have now examined its role in the analogue toward five test bacteria. Deletion of Ile8 reduced activity, and it was not restored by lengthening to 15 residues by addition of another threonine at the C‐terminus. Replacement of Ile8 by a hydrophobic leucine maintained good activity and Ala8 was equally active for four organisms, although less active against Staphylococcus aureus. Replacement by the hydrophilic Ser8 strongly reduced potency against all five organisms. Deletion of Leu15 decreased activity, but addition of Thr16 maintained good activity. The presence of hydrophobic residues appears to have a significant effect on the process of antibacterial activity. These peptide analogues showed voltage‐dependent conductance changes and are capable of forming ion‐pores in planar lipid bilayers. The antibacterial action of the peptides is thought to be first an ionic interaction with the anionic phosphate groups of the membrane followed by interaction with the hydrocarbon core of the membrane and subsequent reorientation into amphipathic α‐helical peptides that form pores (ion‐channels), which span the membrane. The analogue also showed an increase in α‐helicity with an increase in hexafluoro 2‐propanol concentration.
Multiple Column Synthesis of a Library of T‐Cell Stimulating Tn‐Antigenic Glycopeptide Analogues for the Molecular Characterization of T‐Cell–Glycan Specificity
Authors: Frische Klaus , Meldal Morten , Werdelin Ole , Mouritsen Søren , Jensen Teis , Galli‐Stampino Luisa , Bock Klaus
Published: May 2005

A series of peptides and glycopeptides derived by amino acid and glycosyl amino acid scans through the self peptide from CBA/J mouse haemoglobin Hb (67–76), VITAFNEGLK, was synthesized by multiple column peptide synthesis (MCPS). Investigation of glycopeptide binding to the mouse major histocompatibility class II molecule Ek showed that glycans in position 72 did not interfere with the binding to Ek. Immunization experiments revealed that glycopeptides with the glycan in position 72 were immunogenic. Therefore a series of N‐linked and O‐linked glycopeptides with the glycan attached in the position 72 either to serine, threonine or asparagine was synthesized by MCPS. The glycan structure was furthermore varied with respect to monosacc haride component, size of oligosaccharide, anomer configuration and stereoche mistry of essential hydroxyl groups in order to investigate the specificity of the interaction with the T‐cell receptor. Easy synthesis of ready to use Ser and Thr building blocks corresponding to mucin core 1, the Tn‐antigen and its β‐anomer were developed using trichloroacetimidates as glycosyl donors and reduction with in situ acetylation of the azide containing glycosylation products. Synthesis of an α‐linked GlcNAc‐Thr building block was achieved by glycosylation of Fmoc‐Thr‐OPfp with 2‐azido‐2‐deoxy‐3,4,6‐tri‐O‐acetyl‐D‐ glycopyranosyl trichloroacetimidate as a glycosyl donor. Other building blocks were obtained by previously described procedures.
Nonconventional Protease Catalysis in Frozen Aqueous Solutions
Authors: Hänsler Marion , Jakubke Hans‐Dieter
Published: May 2005

During the past decade proteases have been widely used as catalysts in peptide synthesis. Unfortunately, they are not ideal ligases. Enzymatic peptide synthesis in frozen aqueous systems has been developed as an approach towards the suppression of competitive reactions. This paper summarizes reports concerning the behaviour of non‐enzymatic as well as of enzyme‐catalysed reactions when the reaction mixture is frozen. The advantages of freezing the reaction mixture in serine and cysteine protease‐catalysed peptide synthesis, the influence of modified reaction conditions and the possible reasons for the yield‐increasing effect of freezing are discussed.
Current Concepts in Intestinal Peptide Absorption
Authors: Fricker Gert , Drewe Jürgen
Published: May 2005

Today there is considerable interest in oral peptide delivery. However, oral administration of peptides is limited by a low bioavailability and a high variability in plasma levels. A review is given of the literature describing the major barriers in peptide absorption, the basic mechanisms of intestinal peptide transport, the experimental models and the pharmaceutical approaches currently used in the investigation of peptide and protein absorption processes.
The Immunomodulatory Activity of Peptides Related to the DNA Contacting Loop of p53 Protein
Authors: Bolewska‐Pedyczak Eleonora , Siemion Ignacy Z. , Wieczorek Zbigniew
Published: May 2005

Taking into account the sequence homology existing between thymopoietin II and the DNA‐binding domain of p53 protein, a series of octapeptides was synthesized, related to the wild p53 type protein as well as to its mutated forms, appearing in some human tumours. The wild type octapeptide has immunostimulative activity with regard to the humoral immune response, but is inactive in the cellular immune response. The mutated peptides of p53 differ in their immunomodulatory activity from the wild type octapeptide. The Ser5 analogue of the wild type peptide is a strong stimulant of the humoral immune response and enhances TNF‐α production, while at the same time suppressing the cellular immune response. The data suggest that the mutations of p53, which favour tumour development and growth, may also change the immune activity of respective p53 fragments.
An Exploration of the Effects of Constraints on the Phosphorylation of Synthetic Protein Tyrosine Kinase Peptide Substrates
Authors: Ruzza Paolo , Donella‐Deana Arianna , Calderan Andrea , Filippi Bruno , Cesaro Luca , Pinna Lorenzo A. , Borin Gianfranco
Published: May 2005

We synthesized by classical solution methods three conformational constrained analogues of EDNEYTA, a heptapeptide sequence that represents the common major autophosphorylation site of the protein tyrosine kinases (PTKs) of the Src family. The correlation between the different structural properties induced by the modifications of the native sequence and the propensity of the peptides to act as PTK substrates was examined. The kinetic data obtained indicate that the introduction of the tyrosine‐analogue constraints Tic(OH) and MeTyr, which block the ring flexibility, completely prevents the phosphorylation catalysed by the kinases Lyn and Fgr. On the other hand PTKIIB/p38syk can phosphorylate the two derivatives albeit with an efficiency lower than that found with the native sequence. A third derivative contained side chain to side chain cyclization. This analogue, in which the freedom of the phenolic moiety is not altered, can be phosphorylated by all the PTKs tested with kinetic constants comparable to the parent peptide.
Solution Conformation of [D‐Pen2,D‐Pen5]enkephalin in Water: A NMR and Molecular Dynamics Study
Authors: Gußmann Martin , Borsdorf Rolf , Hofmann Hans–Jörg
Published: May 2005

The solution conformation of [D‐Pen2,D‐Pen5] enkephalin (DPDPE), a highly potent δ‐selective opioid agonist, was examined by means of NMR, molecular mechanics and molecular dynamics methods. The structural information in the solvent water was obtained employing one‐ and two‐dimensional methods of1H and13C‐NMR spectroscopy. Based on the distance geometry technique using the ROE data as input, 400 conformers were obtained and considered in the structure analysis. Alternatively, about 2000 conformers were stochastically generated and related to the NMR data after energy minimization. The structure analysis provides one conformer in agreement with all NMR data, which belongs to the lowest energy conformation group. This structure may serve as a reference conformer for DPDPE analogues synthesized with the aim of activity increase.
Preparation of Site‐Specific Isotopically Labelled Zervamicins, the Antibiotic Peptaibols Produced by Emericellopsis Salmosynnemata
Authors: Egorova‐Zachernyuk T. A. , Shvets V. I. , Versluis K. , Heerma W. , Creemers A. F. L. , Nieuwenhuis S. A. M. , Lugtenburg J. , Raap J.
Published: May 2005

A simple procedure for the preparation of the specifically labelled peptide antibiotic zervamicins IC, IIA and IIB has been developed. The zervamicin molecules are labelled with stable isotopes by culturing the Emericellopsis salmosynnemata on a well‐defined synthetic medium containing the highly isotopically enriched amino acid. To obtain the peptide with the specifically and highly enriched amino acid residue, precautions have been taken to prevent any de novo biosynthesis of the particular amino acid from unlabelled precursors. The enrichment of the labelled peptide is determined by mass spectrometric analysis. Following this method we have incorporated [2′,4′, 5′,6′,7′‐2H5]‐L‐Trp‐1, [1′‐15N]‐L‐Trp‐1 and [2′, 3′,4′,5′,6′‐2H5]‐L‐ Phl‐16 into zervamicins IC, IIA and IIB on the preparative scale and without scrambling of the label. Thus, using the procedures described, isotopically labelled zervamicins can be prepared, allowing them to be studied by solid‐ state NMR.
Multivalent Ligand System Carrying Enkephalin and Neurotensin Coimmobilized on Liposomes
Authors: Zhao Jinbao , Kimura Shunsaku , Imanishi Yukio
Published: May 2005

A multivalent ligand system was constructed by coimmobilization of two kinds of peptide ligands, enkephalin and neurotensin derivatives having a dioctadecyl group, on dimyristoylphosphatidylcholine (DMPC) liposomes. The enkephalin derivatives are Tyr‐D‐Ala‐Gly‐Trp‐Leu‐ (Sar‐Sar‐Pro)n‐[N(C18H37)2] (Enk3nD, n=0, 1, 2), where a dioctadecyl group was connected to the C‐terminal side of enkephalin directly or through a hydrophilic and flexible spacer chain of different lengths. The neurotensin derivatives are Ac‐Glu[N(C18H37)2]‐(Sar‐Sar‐Pro)n‐Arg‐Arg‐Pro‐Tyr‐Ile‐Leu‐OH (D3nNT, n=0, 1, 2, 3). The derivatives were spontaneously immobilized on DMPC liposomes by overnight incubation. The receptor affinity of the enkephalin derivatives became significantly higher upon immobilization on liposomes. The highest affinity was obtained for the δ receptor by Enk6D immobilized on DMPC liposomes. This affinity is higher than that of enkephalinamide. Neurotensin derivatives coimmobilized with large amounts of Enk3D on DMPC liposomes show higher affinity than the neurotensin derivatives immobilized alone. The effect of Enk3D on the receptor affinity of the coimmobilized neurotensin derivative disappeared by the addition of [Ala2, MePhe4, Gly‐ol5]enkephalin (DAGO). Therefore, the receptor affinity of a peptide hormone is altered by immobilization on DMPC liposomes and by coimmobilization with other peptide hormones. It was confirmed by fluorescent microscopy that the multivalent ligand system binds to receptors without release of the bound ligands from DMPC liposomes.
Immunogenicity Studies with Haptenated Melittin Peptides: Implication for Membrane Involvement during the Recognition Step
Authors: Curcio‐Vonlanthen Véronique , Rolli Hanspeter , Schneider Conrad H.
Published: May 2005

Melittin peptides carrying 2,4‐dinitro‐6‐carboxyphenyl (Dncp) haptenic groups regularly evoked anti‐hapten IgG responses in mice or guinea pigs when the hapten was C‐terminally attached. Single haptens on the N‐terminal helix in several positions gave poor or no responses in the early stages but adequate titres after prolonged immunization. Peptides with Dncp at the C‐terminus as an invariant feature and a second Dncp in various positions along the peptide chain did not fail to produce adequate responses. The hampering effect is not due to a defect at the T‐cell level but involves the recognition step on the B‐cell. It is implied that the haptenic interaction with the paratope of the recognizing immunoglob ulin on the B‐cell involves the cell membrane in an important way. It is also suggested that late antibody responses should not be overlooked during the development of proteinaceous immunogens for vaccination.
Towards the Understanding of the Folding of Methylene Units in the Glutamine Residue
Authors: Alemán Carlos , Vega M. Cristina , Navarro Eloísa , Puiggalí Jordi
Published: May 2005

The conformational preferences of the methylenic sequence in the side chain of the glutamine residue were investigated by ab initio and semi‐empirical quantum mechanical calculations and examination of both the Brookhaven Protein Databank and Cambridge Structural Data Base. The results were analysed on the basis of our previous findings about the folding of methylene groups in aliphatic segments. Both energy calculations and the crystallographic structure of small peptides indicate that methylene units of the glutamine residue tend to fold in a gauche conformation. In contrast, such groups usually adopt an all‐trans conformation in proteins due basically to the entropic and solvent contributions. These results have been demonstrated by computing the entropic correction to the free energy and evaluating the solvent effects through SCRF calculations
Backbone Cyclization of the C‐terminal Part of Substance P. Part 1: The Important Role of the Sulphur in Position 11
Authors: Bitan Gal , Zeltser Irena , Byk Gerardo , Halle David , Mashriki Yaffa , Gluhov Evgenia V. , Sukhotinsky Inna , Hanani Menachem , Selinger Zvi , Gilon Chaim
Published: May 2005

Novel backbone‐to‐side chain and backbone‐to‐backbone cyclic analogues of substance P (SP) were prepared by solid‐phase synthesis and screened for biological activity. An analogue containing a thioether‐ lactam ring between positions 9 and 11 showed an EC50 value of 20nM toward the neurokinin 1 (NK‐1) and was inactive toward the NK‐2 and NK‐3 receptors. On the other hand, in a multiple backbone cyclic peptide library of similar analogues, in which the sulphur was excluded from the ring, very low activity was detected. The activity was re‐evaluated and was found to be even lower (EC50=0.11 mM) than the previously published data. These results indicate that the thioether moiety has a crucial role in receptor activation. The results also show tolerance of the NK‐1 receptor, but not NK‐2 or NK‐3, to cyclization of the C‐terminal portion of the SP6–11 hexapeptide.
Design of Peptides Using α,β‐Dehydro‐residues: Synthesis, Crystal Structure and Molecular Conformation of N‐Boc‐L‐Val‐ΔPhe–ΔPhe‐L‐Ala‐OCH3
Authors: Bhatia Smita , Dey Sharmistha , Kaur Punit , Singh Tej P.
Published: May 2005

To obtain general rules of peptide design using α,β‐dehydro‐residues, a sequence with two consecutive ΔPhe‐residues, Boc‐L‐Val‐ΔPhe–ΔPhe‐ L‐Ala‐OCH3, was synthesized by azlactone method in solution phase. The peptide was crystallized from its solution in an acetone/water mixture (70:30) in space group P61 with a=b=14.912(3) Å, c= 25.548(5) Å, V=4912.0(6) Å3. The structure was determined by direct methods and refined by a full matrix least‐squares procedure to an R value of 0.079 for 2891 observed [I⩾3σ(I)] reflections. The backbone torsion angles ϕ1=−54(1)°, ψ1= 129(1)°, ω1=−177(1)°, ϕ2 =57(1)°, ψ2=15(1)°, ω2 =−170(1)°, ϕ3=80(1)°, ψ3 =7(2)°, ω3=−177(1)°, ϕ4 =−108(1)° and ψT4=−34 (1)° suggest that the peptide adopts a folded conformation with two overlapping β‐turns of types II and III′. These turns are stabilized by two intramolecular hydrogen bonds between the CO of the Boc group and the NH of ΔPhe3 and the CO of Val1 and the NH of Ala4. The torsion angles of ΔPhe2 and ΔPhe3 side chains are similar and indicate that the two ΔPhe residues are essentially planar. The folded molecules form head‐to‐ tail intermolecular hydrogen bonds giving rise to continuous helical columns which run parallel to the c‐axis. This structure established the formation of two β‐turns of types II and III′ respectively for sequences containing two consecutive ΔPhe residues at (i+2) and (i+3) positions with a branched β‐carbon residue at one end of the tetrapeptide.
Folded Structures in Protonated Reduced Dipeptides
Authors: Grand Vincent , Aubry André , Dupont Virginie , Vicherat André , Marraud Michel
Published: May 2005

Reduced dipeptides with the general formula RCO‐Xaa‐ rXbb‐N+HR′R′′ (rXbb, reduced analogue of residue Xbb: NH‐Cα HR1 ‐Cr H2) are shown to adopt a folded conformation in solution and in the solid state. The protonated reduced amide bond is an active proton donor capable of interacting with a peptide carbonyl to give a strong hydrogen bond topologically equivalent to the i+2 or i+3⇒ i interaction. The resulting conformation is similar to the γ‐ or β‐turn structure found in peptides and proteins.
Cysteine Racemization in Peptide Synthesis: A New and Easy Detection Method
Authors: Siedler Frank , Weyher Elisabeth , Moroder Luis
Published: May 2005

A new method has been developed for the rapid determination of D‐cysteine contents in synthetic peptides. It is based on the reduction of cystine residues, when present, with tris‐ alkylphosphines, selective derivatization of the cysteine residues with 4‐vinylpyridine, followed by acid hydrolysis of the (4‐pyridylethyl)cysteine –peptides. Baseline enantiomeric resolution of theD,L‐S‐β‐(4‐pyridylethyl)cysteine, and thus quantification ofD‐ enantiomer contents at levels ≤1%, is easily achieved by capillary zone electrophoresis exploiting the host–guest complexation principle with crown ethers or by gas chromatography on chiral glass capillary columns upon conventional derivatization of the hydrolysate. The acid‐stability of the (4‐pyridylethyl)cysteine derivative prevents racemization via thiazoline intermediates and allows for standardization of the acid hydrolysis‐dependent racemization.
Beams and plates on elastic foundations: a review
Authors: Wang Y H , Tham L G , Cheung Y K
Published: May 2005

The interaction action between structures and supporting soil media is of fundamental importance in foundation design and it has always attracted the attention of both researchers and engineers. This paper reviews the state‐of‐the‐art in this field, highlighting the key areas of development, including the modelling of the soil media and various analytical as well as numerical approaches in analysing the interaction action between the foundation and soil. Copyright © 2005 John Wiley & Sons, Ltd.
Electrical properties of [Bi1–z(Na1–x–y–zKxLiy)]0.5BazTiO3 multi‐component lead‐free piezoelectric ceramics
Authors: Lin Dunmin , Xiao Dingquan , Zhu Jianguo , Yu Ping
Published: May 2005

A new system of BNT‐based multi‐component lead‐free piezoelectric ceramics, [Bi1–z(Na1–x–y–zKxLiy)]0.5BazTiO3, was prepared by conventional ceramic technique and the electrical properties of the ceramics were studied. The analysis of X‐ray diffraction shows that all ceramics investigated can form a pure perovskite phase. The ceramics exhibit good piezoelec‐ tric performances and strong ferroelectricity: piezoelectric constant d33 = 205 pC/N, electromechanical coupling factor kP = 37.0%, remanent polarization Pr = 38.5 µC/cm2, coercive field Ec = 2.80 kV/mm, and high depolarization temperature Td. It is obvious that [Bi1–z(Na1–x–y–zKxLiy)]0.5BazTiO3 ceramics can be used in practical devices. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)