bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractA 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

AbstractDuring 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

AbstractToday 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

AbstractTaking 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

AbstractWe 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

AbstractThe 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

AbstractA 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

AbstractA 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

AbstractMelittin 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

AbstractThe 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

AbstractNovel 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

AbstractTo 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

AbstractReduced 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

AbstractA 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

AbstractThe 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

AbstractA 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)
Pressure‐induced increase of ionic conduction of water‐treated NaA zeolite
Authors: Secco Richard A. , Goryainov Sergei V. , Huang Yining 
Published: May 2005

AbstractDehydrated, hydrated and superhydrated NaA zeolites have been studied by impedance spectroscopy with scanning frequency from 1 Hz to 1 MHz at high pressure up to 4.5 GPa. A considerable anomalous increase in electrical conductivity in the range of 0.5–1.1 GPa was observed in superhydrated NaA zeolite containing additional water in the channels. A very high mobility of ions in superhydrated zeolite may be associated with the liquid‐like state of the water‐cation stuffing of zeolite channels. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Search for the ground states of Ising spin clusters by using the genetic algorithms
Authors: Oda Akifumi , Nagao Hidemi , Kitagawa Yasutaka , Shigeta Yasuteru , Shoji Mitsuo , Nitta Hiroya , Okumura Mitsutaka , Yamaguchi Kizashi 
Published: May 2005

AbstractGenetic algorithms (GAs) were applied to the search for ground states of randomly generated spin clusters. Two types of hybrid GAs and one type of pure GA modified by crossover operation were developed especially for the search for the ground state on Ising spin clusters. In the hybrid GAs, we used the 1‐neighborhood search and the hill‐climbing search for local searches. For modification of GAs, we also proposed a new crossover operator, x̄ crossover, which turns all spins upside down. The fitness function (F(x)) was defined in terms of the energies obtained by the Ising Hamiltonian. For the Ising spin clusters, the effective magnetic interaction (Jab) values were calculated with the unrestricted Hartree–Fock method. These GAs worked well on the searches for the ground states, because the improved GAs avoided being trapped in the local minima frequently and picked up the global minima more effectively than the standard GAs. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005
Activation of alkanes on zeolites: A DFT study of hydride abstraction and dehydrogenation on extra‐framework aluminum species
Authors: Mota Claudio J. A. , Bhering Daniel L. , Ramírez‐Solís Alejandro 
Published: May 2005

AbstractAn AlOH2+ · T6 cluster was used to represent, at zeroth order, an extra‐framework aluminum species coordinated with the zeolite Y structure. This cluster was used to study the hydride abstraction from alkanes, at B3LYP/6‐311++G(d,p)//B3LYP/6‐31G(d,p) level, to form an alkoxide and an Al‐hydride · T6 species. It was found that all reactions were endothermic with respect to the isolated reactants and presented high activation energy. The endothermicity and activation energy depend on the type of hydride being abstracted. Methane showed the highest values (ΔH = +41.5 kcal/mol and ΔH‡ = 91.7 kcal/mol); isobutane has the lowest (ΔH = +36.8 kcal/mol and ΔH‡ = 46.7 kcal/mol). Dehydrogenation to form an alkene and an adsorbed hydrogen molecule on the AlOH2+ · T6 cluster was also investigated and computed slightly more endothermic than the respective hydride abstraction. However, dehydrogenation showed a significantly lower activation enthalpy, especially for linear alkanes. For isobutane the results indicated a similar energy barrier for hydride abstraction and dehydrogenation. Larger, more realistic clusters and periodic reactivity studies are nevertheless needed to describe, in a more refined way, the energetics of these relevant catalytic reactions in zeolitic systems. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005
On the matching polynomials of graphs with small number of cycles of even length
Authors: Yan Weigen , Yeh Yeong‐Nan , Zhang Fuji 
Published: May 2005

AbstractSuppose that G is a simple graph. We prove that if G contains a small number of cycles of even length then the matching polynomial of G can be expressed in terms of the characteristic polynomials of the skew adjacency matrix A(Ge) of an arbitrary orientation Ge of G and the minors of A(Ge). In addition to a formula previously discovered by Godsil and Gutman, we obtain a different formula for the matching polynomial of a general graph. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005
Ab initio studies on the polarizability of lithium clusters: Some unusual results
Authors: Chandrakumar K. R. S. , Ghanty Tapan K. , Ghosh Swapan K. 
Published: May 2005

AbstractThe polarizability of lithium clusters was studied using ab initio as well as Density Functional Theory (DFT)‐based methods. The electron correlation was found not to play any major role in the evaluation of polarizability of the lithium clusters, contrary to the case of sodium and other types of clusters. The theoretical methods used in the present study are not able to reproduce the unusual features in the size evolution of the polarizability observed experimentally. An interesting feature is that the polarizability of lithium clusters calculated by various methods at 0K temperature is found to be higher than the experimental results measured at higher temperature, which is quite unusual. The significance of these issues is highlighted and the need of highly accurate DFT exchange‐correlation functionals and ab initio methods in the study of the electronic properties of lithium clusters is emphasized. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005
Anisotropy analysis of energy in Ag/Si twist interface
Authors: Xin Hong , Zhang Jian‐Min , Wei Xiu‐Mei , Xu Ke‐Wei 
Published: May 2005

AbstractThe energies in three combinations of Ag(001)/Si(111), Ag(011)/Si(111) and Ag(111)/Si(111) twist boundaries have been calculated using the modified embedded atom method (MEAM). The results show that the interface energies corresponding to Ag(111)/Si(111), Ag(001)/Si(111) and Ag(011)/Si(111) increase successively and the lowest energies 365, 717.7 and 996.1 mJ m−2 corresponding to each interface appear at twist angles θ of 30, 0 and 25.24°, respectively. Considering minimization of interface energy, we can conclude that the Ag films deposited on Si(111) substrate will result in a (111) preferred orientation, especially at a twist angle of θ = 30°. Copyright © 2005 John Wiley & Sons, Ltd.