bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of the conformational domains of bradykinin by computational methods
Authors: Perez Juan J. , Sanchez Yolanda M. , Centeno Nuria B. 
Published: May 2005

AbstractThe AMBER 4.0 force field was used to perform a characterization of the conformational profile of the nonapeptide bradykinin. A thorough conformational search was carried out using molecular dynamics as sampling technique, by computing cycles of high (900 K) and low (300 K) temperature trajectories. A total of 2400 minima were generated and subsequently clustered using the root‐mean‐square of the backbone dihedral angles as criterium. After the use of a tolerance value of 20deg;, the conformations were clustered in 233 unique conformations with energies up to 40 kcal/mol above the lowest minimum. The analysis of the low‐energy conformations indicate that the peptide exhibits a high tendency to adopt a β‐turn at the C‐terminus and a propensity to adopt a bent structure at the N‐terminus. These results are in agreement with the experimental evidence reported in the literature and provide detailed information necessary to understand the conformational preferences of the peptide.
Conformational rigidity versus flexibility in a novel peptidic neurokinin A receptor antagonist
Authors: Pavone Vincenzo , Lombardi Angelina , Maggi Carlo Alberto , Quartara Laura , Pedone Carlo 
Published: May 2005

AbstractNeurokinin A receptor antagonists have been proposed as a new class of drugs for several applications in humans (asthama, intestinal motility, etc.). The rational design, synthesis, structural characterization and biological activity evaluation of a new potent, highly selective, long‐lasting, peptide‐based receptor antagonist are reported. The structure–activity relationship indicates that the conformational rigidity determines potency, specificity and especially the long life of the molecule in the living body. MEN 10627 is the prototype of a new class of cyclic, peptide‐based, neurokinin A receptor antagonists and it is a suitable candidate for clinical testing in humans.
Solution versus solid‐phase cyclization strategies for large sidechain lactam‐bridged peptides: A comparative study
Authors: Camarero Julio A. , Cairó Jordi J. , Giralt Ernest , Andreu David 
Published: May 2005

AbstractA 22‐residue peptide with a sidechain lactam bridge involving 18 residues (60‐atom cycle) has been synthesized. Three different protection schemes using Fmoc/tBu/cyclohexyl, Fmoc/tBu/allyl or Boc/Bzl/ fluorenylmethyl protecting group combinations have been explored for the solid phase of the linear precursors, which have been subsequently cyclized in solution or in the solid phase. Cyclization yields in solution have been consistently better than on solid phase; however, the solid‐phase strategy requires fewer purification steps and therefore global yields are comparable.
Conformational studies on synthetic peptides reproducing the dibasic processing site of pro‐ocytocin–neurophysin
Authors: Di Bello Carlo , Simonetti Mario , Dettin Monica , Paolillo Livio , D'Auria Gabriella , Falcigno Lucia , Saviano Michele , Scatturin Angelo , Vertuani Gianni , Cohen Paul 
Published: May 2005

AbstractSynthetic peptides reproducing the proteolytic processing site of pro‐ocytocin were studied by different spectroscopic techniques, including circular dichroism, Fourier tranform infrared absorption, and mono and bidimensional nuclear magnetic resonance, in order to ascertain the possible role of three‐dimensional structure in the recognition process by maturation enzymes. Experimental results were compared with energy minimization calculations and suggest that: (i) the region situated on the N‐terminus of the Lys‐Arg doublet may form a β‐turn; (ii) the sequential organization of the residues participating in the β‐turn determines the privileged relative orientation of the basic amino acid sidechains and the subtype of turn; and (iii) the peptide segment situated on the C‐terminal side of the dibasic doublet may assume a helix arrangement. These findings, in spite of the limitations connected to the flexibility of linear peptides, seem to substantiate the hypothesis that structural motifs around the cleavage site could be important for recognition and processing. However, a straightforward correlation between details of the secondary structure and the in vitro reactivity toward a putative convertase is not yet possible.
Augmentation of the affinity of HLA class I‐binding peptides lacking primary anchor residues by manipulation of the secondary anchor residues
Authors: Rovero Paolo , Viganò Stefania , Pegoraro Stefano , Revoltella Roberto , Riganelli Daniela , Fruci Doriana , Greco Giulia , Butler Richard H. , Tanigaki Nobuyuki 
Published: May 2005

AbstractA direct binding assay has been used to investigate the effect of the secondary anchor residues on peptide binding to class I proteins of the major histocompatibility complex. Based on predictions from a previous chemometric approach, synthetic peptide analogues containing unnatural amino acids were synthesized and tested for B*2705 binding. Hydrophobic unnatural amino acids such as α‐naphthyl‐ and cyclohexyl‐alanine were found to be excellent substituents in the P3 secondary anchor position giving peptides with very high B*2705‐binding affinity. The binding to B*2705 of peptides optimized for their secondary anchor residues, but lacking one of the P2 or P9 primary anchor residues was also investigated. Most such peptides did not bind, but one peptide, lacking the P2 Arg residue generally considered essential for binding to all B27 subtypes, was found to bind quite strongly. These findings demonstrate that peptide binding to class I proteins is due to a combination of all the anchor residues, which may be occupied also by unnatural amino acids–a necessary step towards the development of peptidic or non‐peptidic antagonists for immunomodulation.
Lactam bridge stabilization of α‐helical peptides: Ring size, orientation and positional effects
Authors: Houston Michael E. , Gannon Cindy L. , Kay Cyril M. , Hodges Robert S. 
Published: May 2005

AbstractA series of 14 residue amphipathic α‐helical peptides, in which the sidechains of glutamic acid and lysine have been covalently joined, was synthesized in order to determine the effect of spacing, position and orientation of these lactam bridges. It was found that although an (i, i+3) spacing would position the lactam bridge on the same face of the helix, these lactams with 18‐member rings were actually helix‐destabilizing regardless of position or location. On the other hand, (i, i+4) lactams with 21‐member rings were helix‐stabilizing but this was dependent on orientation. Glutamic acid‐lysine lactams increased the helical content of the peptide when compared with their linear homologue in benign conditions (50 mM KH2PO4, 100 mM KCl, pH 7). Two Glu‐Lys (i, i+4) lactams located at the N‐ and C‐termini gave rise to a peptide with greater than 99% helical content in benign conditions. Peptides with Lys‐Glu oriented lactams were random structures in benign conditions but in the presence of 50% TFE could be induced into a helical conformation. The stability of the single‐stranded α‐helices, as measured by thermal denaturations in 25% TFE indicated that Glu‐Lys oriented lactam bridges stabilized the helical conformation relative to the linear unbridged peptide. One Glu‐Lys lactam in the middle of the peptide was more effective at stabilizing helical structure than two Glu‐Lys lactams positioned one at each end of the molecule. The lactams with the Lys‐Glu orientation were destabilizing relative to the unbridged peptide. This study demonstrates that correct orientation and position of a lactam bridge is critical in order to design peptides with high helical content in aqueous media.
The application of papain, ficin and clostripain in kinetically controlled peptide synthesis in frozen aqueous solutions
Authors: Hänsler Marion , Ullmann Grit , Jakubke Hans‐Dieter 
Published: May 2005

AbstractThe capability of the cysteine proteases ficin, papain and clostripain to form peptide bonds in frozen aqueous solutions was investigated. Freezing the reaction mixture resulted in increased peptide yields in kinetically controlled coupling of Bz–Arg–OEt with various amino acid amides and dipeptides. Under these conditions, peptide yields increased up to 70% depending on the enzyme and the amino component used. Enzyme‐catalysed peptide syntheses were carried out under optimized reaction conditions (temperature, amino component concentration and pH before freezing) using the condensation of Bz–Arg–OEt and H–Leu–NH2 as a model reaction.
Affinity purification of 101 residue rat cpn10 using a reversible biotinylated probe
Authors: Ball H. L. , Bertolini G. , Mascagni P. 
Published: May 2005

AbstractThe purification of large synthetic peptides using conventional separation techniques often results in poor yields and homogeneity due to the accumulation of chromatographically similar deletion and truncated impurities. We have developed a highly effective synthetic strategy and one‐step purification procedure that is based on (i) the application of single coupling using HBTU/HOBt activation to reduce incomplete couplings, (ii) the use of N‐(2‐chlorobenzyloxycarbonyloxy)succinimide as a capping agent to terminate deletion sequences and (iii) the N‐terminal derivatization of the complete peptidyl‐resin with a reversible Fmoc‐based chromatographic probe possessing enhanced physico‐chemical properties (i.e. hydrophobicity, charge or affinity label). We report the application of a biotinylated probe, activated as the succinimidyl carbonate, for the purification of a 101 residue chaperonin protein from Rattus norvegicus (rat cpn10), previously synthesized using an optimized synthetic protocol. Biotinylated rat cpn10 was separated from underivatized impurities on an immobilized monomeric avidin column. Free rat cpn10 was released from avidin–agarose column with 5% aqueous triethylamine and after desalting by RP‐HPLC gave 9.9% recovery. Characterization and assessment of homogeneity was achieved using ESI‐MS, CZE and RP‐HPLC.
The immunosuppressive mini‐domain of human lactoferrin
Authors: Siemion Ignacy Z. , Sloń Jacek , Wieczorek Zbigniew 
Published: May 2005

AbstractIt has been found that the disulphide‐bridged 231–245 pentadecapeptide loop of the lactoferrin (LF) N‐lobe contains a region of immunosuppressive activity. The activity resides within a thymopentin‐like sequence (Arg‐Lys‐Pro‐Val‐Asp) of the loop. Peptides related to the 575–589 loop of the LF C‐lobe differ in their immunomodulatory activity from those related to the 231–245 loop. We ascribe this difference to the replacement of the Asp residue in the 231–245 loop by Thr in the 575–589 loop. Two other fragments of LF which were studied, 27–34 and 309–315, do not manifest any activy in the DTH test (cellular immune response), but, on testing in vivo, stimulate the humoral immune response. The 27–34 fragment is related to the bactericidal and immunostimulative region of LF identified by Bellamy et al. [1]. Our results show that the LF molecule contains, not only the known immunostimulating mini‐domain, but also a region endowed with immunosuppressive activity.
Synthesis and bioactivity studies of 1‐adamantanamine derivatives of peptides
Authors: Horvat Štefica , Varga‐Defterdarovič Lidija , Horvat Jaroslav , Jukić Ruža , Kantoci Darko , Chung Nga N. , Schiller Peter W. , Biesert Lothar , Pfützner Andreas , Suhartono Haryadi , Rübsamen‐Waigmann Helga 
Published: May 2005

AbstractSmall enkephalin‐related peptides containing a 1‐adamantanamine moiety coupled through an amide linkage at the C‐terminus were synthesized. Several of the compounds showed high μ opioid activity and μ receptor selectivity. The new adamantanamine derivatives were also examined for antiviral activity against HIV‐1 in a cell culture system. Some of them inhibited syncytia formation even when the antigen assay gave evidence for viral replication.
Chemical synthesis of a 7 kDa insect gonadotropic neurohormone
Authors: Girardie Josiane , Girardie Adrien , Van Dorsselaer Alain , Sorokine Odile , Geoffre Serge , Hospital Michel , Precigoux Gilles 
Published: May 2005

AbstractAn original insect neurohormone of 65 residues was synthesized by the solid‐phase methodology using t‐Boc strategy and Boc‐Val‐PAM–resin. The purification, conducted by several steps of liquid chromatography having mass, polarity or charge as separative criteria, yielded the product with the correct molecular weight of 6922 Da determined by mass spectrometry. The synthetic peptide had both the same affinity for the antinative neurohormone serum and the same biological activity as the native neurohormone.
Relationship of sidechain hydrophobicity and α‐helical propensity on the stability of the single‐stranded amphipathic α‐helix
Authors: Monera Oscar D. , Sereda Terrance J. , Zhou Nian E. , Kay Cyril M. , Hodges Robert S. 
Published: May 2005

AbstractThe aim of the present investigation is to determine the effect of α‐helical propensity and sidechain hydrophobicity on the stability of amphipathic α‐helices. Accordingly, a series of 18‐residue amphipathic α‐helical peptides has been synthesized as a model system where all 20 amino acid residues were substituted on the hydrophobic face of the amphipathic α‐helix. In these experiments, all three parameters (sidechain hydrophobicity, α‐helical propensity and helix stability) were measured on the same set of peptide analogues. For these peptide analogues that differ by only one amino acid residue, there was a 0.96 kcal/mole difference in α‐helical propensity between the most (Ala) and the least (Gly) α‐helical analogue, a 12.1‐minute difference between the most (Phe) and the least (Asp) retentive analogue on the reversed‐phase column, and a 32.3°C difference in melting temperatures between the most (Leu) and the least (Asp) stable analogue. The results show that the hydrophobicity and α‐helical propensity of an amino acid sidechain are not correlated with each other, but each contributes to the stability of the amphipathic α‐helix. More importantly, the combined effects of α‐helical propensity and sidechain hydrophobicity at a ratio of about 2:1 had optimal correlation with α‐helix stability. These results suggest that both α‐helical propensity and sidechain hydrophobicity should be taken into consideration in the design of α‐helical proteins with the desired stability.
Conformational behaviour of A cyclolinopeptide a analogue: Two‐dimensional NMR study of cyclo(Pro1‐Pro‐Phe‐Phe‐Ac6c‐IIe‐ala‐Val8)
Authors: Mazzeo Marco , Isernia Carla , Rossi Filomena , Saviano Michele , Pedone Carlo , Paolillo Livio , Benedetti Ettore , Pavone Vincenzo 
Published: May 2005

AbstractThe cyclic octapeptide cyclo[‐Pro1‐Pro‐Phe‐Phe‐Ac6c‐Ile‐ala‐Val8‐] [C8‐Ac6c], containing the Pro1‐Pro‐Phe‐Phe sequence, followed by a bulky helicogenic Cα,α‐dialkylated glycine residue Ac6c (1‐aminocyclohexane‐1‐carboxylic acid), and a D‐Ala residue at position 7 has been synthesized. This cyclic peptide is a deletion analogue of the naturally occurring cyclic nonapeptide cyclolinopeptide A (CLA). It has been designed with the aim of studying the role that the Ac6c and D‐Ala residues play on the conformational behaviour of the whole molecule and their influence on the conformation of the Pro1‐Pro‐Phe‐Phe sequence when compared with cyclolinopeptide A.C8Ac6c has been investigated in chloroform and acetonitrile solutions by 2D NMR techniques. Only one set of sharp signals is observed in both solvents. This evidence strongly supports the hypothesis that only one conformational state exists in the chosen solvents. The interpretation of the experimental data points to the existence for C8‐Ac6c of a very rigid structure stabilized by intramolecular hydrogen bonds. The measured NOE effects allow the calculation of internuclear distances, which have been used as restraints in molecular dynamic calculations. The proposed conformation of the molecule shows that the Pro‐Pro‐Phe segment retains the conformation observed in natural CLA both in solution and in the solid state and that the Ac6c residue indeed reinforces the ring rigidity not permitting the formation of any appropriate cavity in which inorganic cations could be complexed.
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

AbstractFour 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

AbstractThe 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

AbstractThe 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

AbstractA 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

AbstractThe 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.