bluuebunny/crossref_metadata_2025 huggingface dataset:
New hydroxamate inhibitors of neurotensin‐degrading enzymes Synthesis and enzyme active‐site recognition
Authors: BOURDEL ELISABETH , DOULUT SYLVLE , JARRETOU GISELE , LABBE‐JULFIE CATHERINE , FEHRENTZ JEAN‐ALAIN , DOUMBIA O , KITABGI PATRICK , MARTINEZ JEAN
Published: August 2010

Selective and mixed inhibitors of the three zinc metallopeptidases that degrade neurotensin (NT), e.g. endopeptidase 24‐16 (EC 3.4.24.16), endopeptidase 24‐11 (EC 3.4.24.11 or neutral endopeptidase, NEP) and endopeptidase 24‐15 (EC 3.4.24.15), and leucine‐aminopeptidase (type IV‐S), that degrades the NT‐related peptides, Neuromedin N (NN), are of great interest. On the structural basis of compound JMV 390‐1 (N‐[3‐[(hydroxyamino)carbonyl]‐I‐oxo‐2(R)‐benzylpropyl]‐L‐isoleucyl‐L‐leucine), which was a full inhibitor of the major NT degrading enzymes, several hydroxamate inhibitors corresponding to the general formula HONHCO‐CH2‐CH(CH2‐C6H5)CO‐X‐Y‐OH (with X‐Y = dipeptide) have been synthesized. Compound7a(X‐Y = Ile‐Ala) was nearly 40‐times more potent in inhibiting EC 24‐16 than NEP and more than 800‐times more potent than EC 24‐15, with an IC50(12 nM) almost equivalent to that of compound JMV 390‐1. Therefore, this compound is an interesting selective inhibitor of EC 24‐16, and should be an interesting probe to explore the physiological involvement of EC 24‐16 in the metabolism of neurotensin. © Munksgaard 1996.
Structure‐activity studies on C‐terminal hirudin peptides containing sulfated tyrosine residues
Authors: MURAMATSU RYO , KOMATSU YASUHIKO , NUKUI ERIKO , OKAYAMA TORU , MORIKAWA TADANORI , KOBASHI KYOICHI , HAYASHI HIDEYA
Published: August 2010

To clarify the role of the negative charge of the C‐terminal region of hirudin, we chemically synthesized the C‐terminal peptide of hirudin variant‐1 (HV‐1), HV‐1‐(54‐65), and its analogs, [E61Y,E62Y]HV‐1‐(54‐65) and [E62Y]HV‐1‐(54‐65), and then sulfated the Tyr residue(s) in these peptides by both enzymic and chemical methods. Enzymic O‐sulfation of Tyr residues in the peptides by use of sulfotransferase isolated from Eubacterium A‐44 allowed us to produce four kinds of the sulfated peptide, whose C‐terminal sequences were ‐PEY(SO3H)YLQ, ‐PYY(SO3H)YLQ, ‐PYYY(SO3H)LQ and ‐PYY(SO3H)Y(SO3H)LQ. On the other hand, all Tyr residues in the peptides were successfully sulfated by chemical reaction with N, N′‐dicyclohexylcarbodiimide in the presence of sulfuric acid. Based on the analysis of structure‐activity relationships of these sulfated peptides for thrombin inhibition, the Tyr62 and Tyr63 bisulfated peptide GDFEEIPEY(SO3H)Y(SO3H)LQ was found to be the most potent inhibitor of thrombin among the products tested. No increase in potency was observed by further substitution of Glu61 with Tyr(SO3H). The inhibitory activity by substitution with Tyr(SO3H) at position 63 was greater than that obtained by the substitution at position 62. © Munksgaard 1996.
The pressure‐induced structural change of bovine α‐lactalbumin as studied by a fluorescence hydrophobic probe
Authors: TANAKA NAOKI , NAKAJIMA KAZUHIRO , KUNUGI SHIGERU
Published: August 2010

The effect of pressure on bovine α‐lactalbumin (LA) has been investigated by fluorescence methods. The intrinsic fluorescence spectra of holo‐LA (CaII‐bound LA) hardly changed in its intensity and maximum wavelength on increasing the pressure up to 400 MPa. In the intrinsic fluorescence spectrum of apo‐LA (CaII‐depleted form) the maximum wavelength was red‐shifted, and the intensity was increased to a large extent by increasing pressure. The fluorescence titrations of both forms of LA were performed with a fluorescent hydrophobic probe 1,1′‐bis(4‐anilino)naphthalene‐5,5′‐disulfonate (bis‐ANS) at various pressures, and binding constants (Kb) of bis‐ANS were calculated. The Kb‐Value for holo‐LA slightly decreased from 0.1 to 100 MPa and increased above 200 MPa. The Kb value for apo‐LA gradually increased with increasing pressure up to 400 MPa. These results were explained by the difference in hydrophobic characteristics of holo‐ and apo‐LA. © Munksgaard 1996.
Stereoselective syntheses of 3‐mercaptoproline derivatives protected for solid phase peptide synthesis
Authors: KOLODZIEJ STEPHEN A. , MARSHALL GARLAND R.
Published: August 2010

The incorporation of cis‐ and trans‐3‐mercaptoproline (3‐MPc and 3‐MPt) into analogs of biologically active peptides has been shown to be an effective means for reducing the conformational mobility of the peptide backbone. We report herein a novel stereoselective synthetic route to l‐1 and l‐2, derivatives of 3‐MPt and 3‐MPc suitably protected for solid phase peptide synthesis. The optically active starting material was the previously reported cis‐3‐hydroxyprolinol derivative l‐3. Oxidation of the C1 alcohol to the carboxylic acid, formation of the methyl ester and deprotection of the C3 alcohol yielded l‐6 in an overall yield of 68%. Reaction of the secondary alcohol with thiolacetic acid under Mitsunobu conditions gave the thiolacetate l‐7 in 77% yield with clean inversion of configuration. Conversion of l‐7 to l‐1 was accomplished in a one‐pot sequence consisting of three steps: hydrolysis of the thiolacetate, formation of the thioether and hydrolysis of the methyl ester. The overall yield of l‐1 from l‐3 was 38%. Synthesis of l‐2 required an epimerization of l‐6, which was accomplished using a standard Mitsunobu inversion to give the trans‐3‐hydroxyproline derivative l‐8. Transformation of l‐8 to l‐2 followed that described for l‐1, except that removal of the methyl ester from l‐10 required acidolysis in refluxing 4N HCl. The overall yield of l‐2 from l‐3 was 18%. The availability of pure enantiomers of 3‐MPt and 3‐MPc protected for SPPS will greatly facilitate their use as conformational constraints for studying peptide‐receptor interactions. © Munksgaard 1996.
Side reactions in solid‐phase peptide synthesis and their applications
Authors: HSIEH KUN‐HWA , DEMAINE MARGARET M. , GURUSIDAIAH S.
Published: August 2010

Side reactions in peptide synthesis indicate steps needing improvement as well as opportunities for structural diversification in combinatorial design. Among the side reactions observed in this study, transesterification of Boc‐Glu(OBzl) occurred in TMAH‐catalyzed resin attachment, leading to Boc‐DKKREE(OMe) in solid‐phase synthesis of Boc‐DKKREE. Acetylation of Boc‐Arg(NO2)‐resin occurred during resin capping with Ac2O/Et3N, leading to GPR(Ac) in GPR synthesis. His‐ and Lys‐modification occurred during GHRPLDKKREE cleavage from resin by Pd(OAc)2‐catalyzed hydrogenation in DMF. To verify these side reactions, model experiments were performed, which indicated rapid transesterification of Boc‐Glu(OBz1) in methyl. isopropyl, or tert‐butyl alcohol into the corresponding ester by TMAH, but not by Cs. This TMAH ability was used to devise a convenient procedure for peptide cleavage. TLC studies of acetylation showed that both Boc‐Arg(NO2) and Boc‐Arg(Tos) were stable to Ac‐Im treatment, but were modified by Ac2O/Et3N. Since transfer hydrogenation of Boc‐His(Bzl) and Boc‐Lys(Z) in HCOOH or ammonium formate did not generate the formylated side‐products of catalytic hydrogenation, DMF and not its decomposed product, HCOOH, appeared involved in side‐chain modification. Elimination of the side reactions, by using Cs‐derived Boc‐Glu(OBzl)‐resin for peptide synthesis and catalytic hydrogenation in NMP‐HOPr for peptide cleavage. increased the GHRPLDKKREE yield by 1/3. On the other hand, the side reactions provided modified peptides, whose bioassays revealed different importance of the modified side‐chains. © Munksgaard 1996.
Conformational investigation of α,β‐dehydropeptides VII*. Conformation of Ac‐Pro‐ΔAla‐NHCH3 and Ac‐Pro‐(E)‐ΔAbu‐NHCH3: comparison with (Z)‐substituted α,β‐dehydropeptides†
Authors: PIETRZYŃASKI C. , RZESZOTARSKA B. , CISZAK E. , LISOWSKI M. , KUBICA Z. , BOUSSARD G.
Published: August 2010

The crystal structure and solution conformation of Ac‐Pro‐ΔAla‐NHCH3 and the solution conformation of Ac‐Pro‐(E)‐ΔAbu‐NHCH3 were investigated by X‐ray diffraction method and NMR, FTIR and CD spectroscopies. Ac‐Pro‐ΔAla‐NHCH, adopts an extended‐coil conformation in the crystalline state, with all‐trans peptide bonds and the ΔAla residue being in a C5 form, φ1=– 71.4(4), ψ1=– 16.8(4), φ2=– 178.4(3) and ψ2= 172.4(3)°. In inert solvents the peptide also assumes the C5 conformation, but a γ‐turn on the Pro residue cannot be ruled out. In these solvents Ac‐Pro‐(E)‐ ΔAbu‐NHCH3 accommodates a βII‐turn, but a minor conformer with a nearly planar disposition of the CO—NH and C=C bonds (φ2∼0°) is also present. Previous spectroscopic studies of the (Z)‐substituted dehydropeptides Ac‐Pro‐(Z)‐ ΔAbu‐NHCH, and Ac‐Pro‐ΔVal‐NHCH3 reveal that both peptides prefer a βII‐turn in solution. Comparison of conformations in the family of four Ac‐Pro‐ΔXaa‐NHCH3 peptides let us formulate the following order of their tendency to adopt a β‐turn in solution: (Z)‐ ΔAbu > (E)‐ δAbu > ΔVal; ΔAla does not. None of the folded structures formed by the four compounds is stable in strongly solvating media. © Munksgaard 1996.
An effective organic solvent system for the dissolution of amino acids
Authors: MITIN YURI V.
Published: August 2010

Dimethylformamide containing strong acids (CF3 COOH, HBF4. TosOH, etc.) and an excess of tertiary base with pK≤6 is an effective solvent system for the dissolution of amino acids and their derivatives. The preferable base is pyridine, which forms a system with an apparent pH of 5.3. Amino acids dissolved in this solvent system readily interact with acylating reagents (BOC2O, ZOSu, Fmoc‐OSu and activated derivatives of N‐protected amino acids). A number of BOC‐, Z‐, Fmoc‐amino acids, as well as several dipeptides, were synthesized using this solvent system with 80‐99%) yields. © Munksgaard 1996.
Motifs and conformational analysis of amino acid residues adjoining β‐turns in proteins
Authors: RAMAKRISHNAN C. , SRINIVASAN N. , NATARAJ D.V.
Published: August 2010

Using a data set of 250 non‐homologous high‐resolution globular proteins, a systematic analysis of the conformations that precede and succeed (positions i and i+3) the various classical β‐turn types has been carried out. The collective conformation of a specific β‐turn type, including the flanking positions, termed motif, has been studied. In all the four turn types, the majority of examples are preceded and succeeded by extended conformation. Some of the other observations are: (1) In a type I β‐turn, Gly at position i+ 3 has a higher favorability to occur with positive ø and does not prefer the major motif βαR‐αR‐β. (2) The left‐handed alpha;‐helical conformation (alpha;L) is not preferred at both the flanking positions for type I'and II β‐turns, (3) The β–β motif is favourable for all the turn types and the motif β–αL very highly favourable for type I. © Munksgaard 1996.
Hydrophobic distribution and spatial arrangement of amino acid residues in membrane proteins
Authors: GROMIHA M. ICHAEL , PONNUSWAMY P.K.
Published: August 2010

The analysis of known three‐dimensional structures of membrane proteins provides an opportunity to understand their structure and stability. In this article we analyse the hydrophobic variation of amino acid residues at various ranges in membrane and aqueous parts of membrane proteins. The numerical indices for several properties of amino acid residues in membrane proteins, such as surrounding hydrophobicity, gain in surrounding hydrophobicity, hydrophobic gain ratio, accessible surface area, preference of amino acid residues in the interior and surface parts, solvent accessible reduction ratio and buriedness, were set up. The relative preference of amino acid residues at various positions of membrane proteins were obtained in a very realistic approach. © Munksgaard 1996.
Solid‐phase synthesis, metal binding and folding properties of caulimovirus‐related ‘zinc finger’
Authors: JI HONG , ZHANG RUOHENG , LAI LUHUA , SHAO MEICHENG
Published: August 2010

A 17‐residue peptide containing the caulimovirus‐related ‘zinc finger’ was prepared by solid‐phase peptide synthesis. Fluorescence measurements showed that the tryptophan quantum yield was Zn2+ ‐dependent, allowing a 1:1 stoichiometry for the complex to be determined. The structure of the peptide was characterized using circular dichroic spectroscopy, which indicates that the peptide exhibits a random coiled conformation in the absence of zinc but appears to form an ordered structure in the presence of zinc. © Munksgaard 1996.
Kinetics of inhibition of aminoacylase activity by dithiothreitol or 2‐mercaptoethanol
Authors: YANG YI , WANG HONG‐RUI , ZHOU HAI‐MENG
Published: August 2010

The previously described kinetic method of the substrate reaction during irreversible inhibition of enzyme activity [Tsou (1988) Adv. Enzymol. Relat. Areas Mol. Biol.61. 381–436] has been used to study the inactivation kinetics of aminoacylase by dithiothreitol (DTT) and 2‐mercaptoethanol (MET). The results show that the inactivation of aminoacylase by DTT or MET is competitive slow‐reversible inhibition. The microscopic rate constants for the inactivation reaction were determined. Removal of these inhibitors by dialysis can lead to complete recovery of enzymatic activity. The present results also show that the presence of equimolar Zn2+ to DTT gives complete protection of the enzyme against the inactivation by DTT. Moreover, addition of equimolar amounts of Zn2+ to DTT can induce recovery of the enzymatic activity of DTT‐inactivated enzyme. It is known that aminoacylase from pig kidney contains no disulfide bonds. Therefore, it may be suggested that inactivation of aminoacylase by dithiothreitol or 2‐mercaptoethanol is not due to the reduction of disulfide bonds, and is a competitive slow‐reversible inhibition.
Interaction of 5,7‐dihydroxy‐4′‐methoxyflavone with a multisubunit protein, carmin: thermodynamics and kinetics of interaction
Authors: RAO K. SUDHINDRA , SURYAPRAKASH P. , PRAKASH V.
Published: August 2010

Acacetin (5,7‐dihydroxy‐4‐methoxy flavone) is a flavone intrinsically present in the seeds of Carthamus tinctorius. Carmin is a multimeric, high molecular weight protein from the seeds of Carthamus tinctorius. The association constant of interaction of acacetin and carmin is maximum at 37.2 °C with a value of (3.96±0.61)× 104 M−1 as measured by fluorescence quenching. Acacetin has at least two binding sites on carmin. The interaction follows pseudo‐first‐order kinetics with a reaction rate constant of 3.4 ± 0.4 s−1. The titration calorimetric data suggest that binding sites for acacetin and its structural analogue, biochanin A, are conserved. The interaction does not affect the association‐dissociation equilibrium of the protein. Also, the binding does not induce any significant conformational changes in the protein as monitored by circular dichroic spectra. Biochanin A (5,7‐dihydroxy‐4′‐methoxyisoflavone), a structural analogue, interacts with carmin with an association constant of (9.33 ± 1.44) × 104 M−1 at 36.9 °C. This indicates that the stereochemistry of the ligand plays an important role in the binding process of flavone to protein. Interaction studies of chemically modified lysyl and tryptophanyl groups separately, and lysyl and tryptophanyl groups sequentially, in the protein carmin with the ligands reveal the involvement of tryptophanyl residues in the binding process and show that it is predominantly an entropically driven hydrophobic interaction. © Munksgaard 1996.
Solid‐phase synthesis and conformational studies of helper T cell immunogenic peptides that carry carbohydrate haptens linked to serine
Authors: ELOFSSON MIKAEL , WALSE BJÖRN , KIHLBERG JAN
Published: August 2010

N
α‐Fmoc serine and its corresponding pentafluorophenyl ester were glycosylated with the 1,2‐trans peracetates of the disaccharides galabiose and cellobiose. Complete stereoselectivity and 52‐75% yields were obtained under boron trifluoride etherate promotion. Lower yields and loss of stereoselectivity were obtained when thioglycosides. trichloroacetimidates or glycosyl bromides were employed as glycosyl donors. The glycosylated building blocks were used in solid‐phase synthesis of derivatives of a helper T cell immunogenic peptide consisting of amino acids 52‐61 from hen‐egg lysozyme. 1H‐NMR spectroscopy in DMSO‐d6 showed that the peptide moiety of the glycopeptides assumed random conformations which were not influenced by glycosylation at different positions.
Properties of synthetic analogs of gramicidin S containing L‐serine or L‐glutamic acid residue in place of L‐ornithine residue
Authors: TAMAKI MAKOTO , AKABORI SADATOSHI , MURAMATSU ICHIRO
Published: August 2010

In order to investigate the biological role of the δ‐amino groups of the Orn residue in gramicidin S, the four analogs, [Ser2]‐, [Ser2,2′]‐, [Glu2]‐ and [Glu2,2′]‐gramicidin S were synthesized by a solution method. Except for the last one, these analogs show antibiotic activity to a certain extent against gram‐positive micro‐organisms, but the activities are weaker than that of gramicidin S. These results indicate that the δ‐amino group of the Orn residue is quite important for exhibiting of the activity of gramicidin S, but is not essential to the activity. NMR and CD studies of these analogs indicate that these analogs possess four intramolecular hydrogen bonds between the Val and Leu residues similar to those of GS, and the removal or diminution of the δ‐amino group of ornithine residues give the considerable influence to the dihedral angle of NαH‐CαH of D‐Phe residues and consequently affect the type II′β‐turn structure of the cyclic peptides. © Munksgaard 1996.
Conformational and electrostatic properties of V‐G‐G‐V‐G, a typical sequence of the glycine‐rich regions of elastin An ab initio quantum molecular study
Authors: BROCH H. , MOULABBI M. , VASILESCU D. , TAMBURRO A.M.
Published: August 2010

The conformational analysis and electrostatic properties of the monomeric sequence V‐G‐G‐V‐G of the glycine‐rich regions of elastin is presented with the aim of explaining NMR and CD experimental results. On the basis of the molecular model NH3−‐V‐G‐G‐V‐G‐COO−, Gaussian 92 quantum‐molecular computations were performed by using principally an ab initio method at the 3‐21G level and AM1. The occurrence of local secondary structures and of βI, βII, βII′ and VIa turns is discussed. Our results clearly demonstrate that the transconformations βI → half turn (which was invoked to explain experimental results) and βI→βII′ are theoretically allowed. © Munksgaard 1996.
Multipin solid‐phase synthesis of acyl 2,3‐diaminopropionic acid oligomers
Authors: VALERIO ROBERT M. , BRAY ANDREW M. , STEWART KAREN M.
Published: August 2010

A modular approach for the synthesis of sets of diverse organic molecules is described. N‐α‐Fmoc‐N‐β‐Alloc‐D‐2,3‐diaminopropionic acid (Fmoc‐D‐Dpr(Alloc)‐OH) was prepared in four steps from BOC‐D‐asparagine and used as a scaffold for attachment of sidechains. Using the Multipin approach, a number of model acyl trimers were rapidly prepared by sequential coupling of Fmoc‐D‐Dpr(Alloc)‐OH and acylation of the β‐amino group with a range of activated carboxylic acids. © Munksgaard 1996.
Purification and mass spectrometry‐based sequencing of yellow mustard (Sinapis alba L.) 6 kDa proteins Identification as antifungal proteins
Authors: NEUMANN GREGORY M. , CONDRON ROSEMARY , POLYA GIDEON M.
Published: August 2010

Three basic proteins, M1, M2A and M2B, that are substrates for plant Ca2+ ‐dependent protein kinase (CDPK) were purified from seeds of yellow mustard (Sinapis alba L.) by a protocol involving batchwise chromatography on carboxymethylcellulose (CM52), cation‐exchange HPLC on an SP5PW column and reversed‐phase HPLC on a C18 column. The complete amino‐acid sequences of these proteins have been determined employing Edman sequencing and electrospray ionization mass spectrometry (ESMS) applied to the proteins and their tryptic and chymotryptic fragments. M1 (observed mass 5676.8 ± 1.0 Da; calculated mass 5677.57 Da), M2A (observed mass 5704.8 ± 0.8 Da; calculated mass 5704.60 Da) and M2B (observed mass 5839.5 ± 1.2 Da; calculated mass 5838.78 Da) have been identified as γ‐thionins, which are potent antifungal proteins. M1, M2A and M2B are phosphorylated by plant CDPK on Ser residues, the site of phosphorylation on M2A being S8 as directly confirmed by Edman sequencing and mass spectrometry of the chymotryptically generated phosphopeptide CQRPS(HPO3)GTW11. M1 and M2A have apparent calmodulin (CaM) antagonist activity with IC50 values of 4.8 ± 1.3 μM and 5.5 ± 1.5 μM, respectively, for inhibition of CaM‐dependent myosin light chain kinase (MLCK). M2A and/or M2B interacts with dansyl‐CaM in both the presence and absence of calcium. © Munksgaard 1996.
1H NMR studies of prototypical helical designer peptides A comparative study of the amide chemical shift dependency on temperature and polypeptide sequence
Authors: VINOGRADOV ALEX A. , MARÍ FRANK , HUMPHREYS ROBERT E. , WRIGHT GEORGE E.
Published: August 2010

A series of designer α‐helical peptides with hydrophobic residues located at different positions along the sequence (PH‐1.0 =LYQELQKLTQTLK, PH‐1.19 =LYQELQKLTQTLFK, PH‐1.12 =LYQELQKLLQTLK,PH‐1.13 =LYQELQKLTLTLK,PH‐1.4 =LYQELQKLTQTTK) were analyzed using one‐ and two‐dimensional NMR methods (TOCSY and NOESY). The central feature of these designer peptides is the incorporation of a maximal hydrophobic strip which may play a role in antigen processing and the nucleation of α‐helices in proteins (J. Immunol.145, 899, 1990). Using the 2D‐NMR, sequence specific assignments and NOE connectivities were determined in all peptides when dissolved in H2O/TFE mixtuRes NOE connectivities indicated that all these peptides are helical in this medium. An unusually large number of NOEs was found for all these designer peptides. This is in accord with ultracentrifugation studies that showed that PH‐1.0 forms a trimer in 50% H2O/TFE mixtures. Other peptides in the series behave in similar manner as PH‐1.0. The structural differences among these peptides was addressed using the backbone amide chemical shift temperature coefficients, ∇, and the differences between the observed and random coil values, ΔδHN. The ΔδHN patterns along the peptide sequence are consistent with those expected for amphiphilic α‐helices, where most ΔδHN values are below zero. However, no significant differences among the peptides in this series can be detected on the ΔδHN patterns, with the exception of PH‐1.12. The ∇ values reveal differences among the peptides of the series. The patterns of ∇ along the peptide sequences are similar to that found for ΔδHN for PH‐1.0, PH‐1.19 and PH‐1.4. The other peptides in the series, PH‐1.12 and PH‐1.13, showed different patterns for ∇. The latter parameter was used to evaluate the helicity of this series of peptides. According to this parameter the relative helicity of this series is as follows: PH‐1.12 < PH‐I .O < PH‐1.4 < PH‐1.19 < PH‐1.13 The NMR data shown here correlated well with the helical propensities predicted for polypeptide sequences using statistical arguments (Proc. Nutl. Acad Sci. USA, 90, 9100, 1993). 0 Munksgaard 1996.
Conformational analysis of human growth hormone [6‐13] peptide analogues
Authors: HIGGINS KERRY A. , THOMPSON PHILIP E. , HEARN MILTON T.W.
Published: August 2010

The conformational analysis of a series of ten hGH[6‐13] peptide analogues is reported. As part of our earlier studies, the x‐aminosuccinimide modified fragment Asu11‐hGH[6‐l3] has previously been identified as a potentiator of insulin activity in intravenous insulin tolerance tests, and various analogues have been subsequently designed, synthesised and employed to acquire structure‐activity data. These studies have lead to the conclusion that the conformational characteristics at the C‐terminus of each of the active peptide analogues is important to the biological activity. In the present investigation, molecular dynamics and simulated annealing techniques have been used to examine the accessible conformational states of the C‐terminal region of ten different hGH[6‐13] peptide analogues. Of these six are active peptide analogues while the other four show no biological activity. Examination of the conformer groups identified using this molecular dynamics approach showed a common conformational motif for each of the active peptides. © Munksgaard 1996.
Opioid receptor affinity of multivalent ligand system consisting of polymerized liposome
Authors: TETSUI SHOKO , ZHAO JINBAO , KIMURA SHUNSAKU , IMANISHI YUKIO
Published: August 2010

A multivalent ligand system, in which enkephalin/phospholipid conjugates were immobilized on a polymerized liposome, has been prepared. A hydrophilic spacer chain, ‐(Sar‐Sar‐Pro)2‐, was placed between Tyr‐D‐Ala‐GIy‐Trp‐Leu (an enkephalin part) and a phospholipid part to diminish steric hindrance of the liposome against receptor binding of the enkephalin unit. The affinity of the immobilized enkephalin conjugate for opioid receptor was dependent on the density of the enkephalin unit on the surface of polymerized liposome, indicating that more than two enkephalin units on a liposome simultaneously bind to receptors in the membrane. IC50 values for the §‐ and μ‐receptors were 15 and 26 nM, respectively, when the conjugate was immobilized at the molar ratio of [enkephalin]/[phospholipid] of 340. The latter affinity is better than that of Tyr‐D‐Ala‐Gly‐Trp‐Leu (50 nM). The enkephalin part was located at the membrane surface, as indicated by fluorescence spectroscopy. When 12% cerebroside sulfate was mixed in the polymerized liposome, §‐receptor affinity of the immobilized enkephalin conjugate was improved to 7.4 nM. The environment around the enkephalin part became hydrophilic upon incorporation of cerebroside sulfate into the polymerized liposome, resulting in changes in the receptor affinities. © Munksgaard 1996.
Conformational comparison in the snake toxin family
Authors: FALKENSTEIN ROBERTO J. , PEÑA CLARA , DE JIMÉNEZ BONINO MIRTHA J. BISCOGLIO
Published: August 2010

A theoretical method was applied to consensus sequences of several members of the snake toxin family as a further approach to examining their conformational homology. Some secondary‐structure predictions as well as hydropathy profiles were also examined. A comparison of long neurotoxins themselves reveals a high homology degree. However, their C‐terminal fragments show poor homology and the N‐terminal fragments appear as the region of maximum variability. Moreover, when the matrix includes the consensus sequence of the genus Laticauda (LNTX1), lacking the disulfide bridge 31–35, the method detects a lower conformational homology in a molecular region centered at position 31. Unlike long neurotoxins, the N‐terminal segments of short neurotoxins show a high homology degree, but when comparing short with long neurotoxins, a poor correlation is found in this zone of the molecule. Cytotoxins studied exhibit an excellent conformational homology except when the consensus sequence of cytotoxin homologues CTXE is one of the proteins in the matrix. A comparison between cytotoxins and short neurotoxins reveals homology only in two segments belonging to a β‐sheet structure. A considerable degree of homology is found between the short neurotoxin group and calciseptin and fasciculin as well as between the long neurotoxin group and κ‐neurotoxins. © Munksgaard 1996.
Steric constraints in the recognition of peptide substrates for the epidermal growth factor receptor kinase
Authors: TONG KIRK , GUYER CHERYL A. , STAROS JAMES V.
Published: August 2010

Epidermal growth factor (EGF) stimulates cellular mitogenesis by binding to and activating its membrane‐associated receptor. An important component of signal transduction by the activated receptor is the stimulation of an intrinsic tyrosyl residue‐specific protein kinase, which selectively phosphorylates tyrosyl residues in the cytoplasmic tail of the receptor and in other cytoplasmic substrates. A recent study utilizing tyrsub, a new high affinity synthetic peptide substrate for the EGF receptor kinase, provided evidence that in peptide substrate binding, the tyrosyl residue plays the central role in recognition, with residues surrounding the tyrosyl residue contributing to stabilization of docking [Guyer et al. (1994) Arch. Biochem. Biophys.312, 573–578], A large body of previous work had identified acidic residues near the site of phosphorylation as most important for binding; therefore, other residues in tyrsub appeared to be promising sites for locating spectroscopic reporter groups. Since tyrsub has neutral residues –4 and + 4 residues from the site of phosphorylation, we prepared two analogs of tyrsub, in each of which one of those residues was substituted with Cys. These cystyrsubs were found to be effectively phosphorylated by EGF receptor prepared from A431 cells, on stimulation with EGF, with high affinities [Km(app)= 40–50 μM]. Modification of the cystyrsubs with iodoacetamide had no deleterious effect on the ability of the peptide to be phosphorylated by the EGF receptor kinase, while the labeling by 5‐iodoacetimidofluorescein completely abolished the productive interaction between the peptide and the EGF receptor. This unexpected failure of the fluorescently labeled peptides to be phosphorylated does, however, provide information on steric limitations to recognition of substrates by the EGF receptor kinase. ©Munksgaard 1996.
Solid‐phase synthesis of H‐ and methylphosphonopeptides
Authors: HOFFMANN RALF , THOLEY ANDREAS , HOFFMAN THOMAS , KALBITZER HANS ROBERT
Published: August 2010

We introduce solid‐phase syntheses of H‐ and methylphosphonopeptides, giving access for the first time to a new class of mimics for o‐phosphoamino acids. The model peptides H‐GlyGlyXaaAla‐OH (Xaa = Ser, Thr) were synthesized on a solid‐phase using Fmoc/tBu strategy and HBTU/HOBt activation by incorporation of hydroxyl‐protected serine and threonine. As selectively cleavable hydroxyl‐protecting groups we used triphenylmethyl and tert‐butyldimethylsilyl for both amino acids, as described in the literature. All peptides were phosphitilated with O,O‐di‐tert‐butyl‐N,N‐diethylphosphoramidite and yielded H‐phosphonopeptides after trifluoroacetic acid cleavage. Alternatively we phosphonylated the peptides with O‐tert‐butyl‐N,N‐diethyl‐P‐methylphosphonamidite, which was synthesized by a two‐step one‐pot procedure starting from commercially available chemicals. All H‐ and methylphosphonopeptides were obtained in high purities and yields, as shown by reversed‐phase high‐performance liquid chromatography and anion‐exchange chromatography.

The phosphonopeptides were characterized by 1H and 31P NMR. We confirmed their molecular masses by electrospray mass spectrometry and analyzed their fragmentation schemes, which seemed to be characteristic for each class of analogues. The H‐phosphonopeptides lost phosphonic acid (H3PO3, 82 mass units) and the methylphosphonopeptides lost methylphosphonic acid (MeH2PO3, 96 mass units). Both H‐ and methylphosphonopeptides represent a new and simply accessible class of mimics for phosphopeptides. Compared with the corresponding phosphopeptides all phosphonopeptides were synthesized in higher yields and purities (>80%). © Munksgaard 1996.
Dermal fibroblasts contribute to multiple tissues in the accessory limb model
Authors: Hirata Ayako , Gardiner David M. , Satoh Akira
Published: August 2010

The accessory limb model has become an alternative model for performing investigations of limb regeneration in an amputated limb. In the accessory limb model, a complete patterned limb can be induced as a result of an interaction between the wound epithelium, a nerve and dermal fibroblasts in the skin. Studies should therefore focus on examining these tissues. To date, however, a study of cellular contributions in the accessory limb model has not been reported. By using green fluorescent protein (GFP) transgenic axolotl tissues, we can trace cell fate at the tissue level. Therefore, in the present study, we transgrafted GFP skin onto the limb of a non‐GFP host and induced an accessory limb to investigate cellular contributions. Previous studies of cell contribution to amputation‐induced blastemas have demonstrated that dermal cells are the progenitors of many of the early blastema cells, and that these cells contribute to regeneration of the connective tissues, including cartilage. In the present study, we have determined that this same population of progenitor cells responds to signaling from the nerve and wound epithelium in the absence of limb amputation to form an ectopic blastema and regenerate the connective tissues of an ectopic limb. Blastema cells from dermal fibroblasts, however, did not differentiate into either muscle or neural cells, and we conclude that dermal fibroblasts are dedifferentiated along its developmental lineage.
Note on Water Drag on Sea Ice for Different Surface
Roughness
Authors: Myrhaug D.
Published: August 2010

The approach in Myrhaug [1], where a simple analytical theory describing the motion in a turbulent planetary boundary layer near a rough seabed was presented, is extended to smooth and transitional smooth-to-rough turbulent flow. An inverted boundary layer similar to that at the seabed is applicable under the sea ice. The water drag coefficient at the ice surface and the direction of the surface shear stress are presented for rough, smooth and transitional turbulent flows.
Model Tests on Multi-Tube Production Risers
Authors: Hartnup G. C. , Airey R. G.
Published: August 2010

Model tests carried out at 1/14.5 scale on two production risers in a towing tank are described. One of the risers considered is modeled on that used in the Buchan field, while the other has a compact low drag configuration of the same production capacity. The tensioning system was carefully modeled, and vessel surge motions were accurately represented in both regular and irregular waves. Current was represented by carriage motion. Some results are presented for bending moments and displacements for both models and comparisons are made with computer simulations to deduce appropriate values for hydrodynamic coefficients.
Wave Interaction With a Rectangular Pit
Authors: Williams A. N. , Vazquez J.
Published: August 2010

A Green function approach is utilized to investigate wave interaction with a rectangular pit of finite dimensions in water of otherwise constant depth. The fluid domain is divided into two regions: an interior region which is finite in extent and represents the pit itself, and an exterior region consisting of the remainder of the fluid domain. An integral equation solution utilizing an appropriate Green function in the exterior region is linked to an interior solution in the form of a Fourier expansion containing unknown potential coefficients through matching conditions at the imaginary interface between the two regions. Discretizing the integral equation leads to a matrix system for these potential coefficients which may be solved using standard matrix techniques. Numerical results are presented for several example geometries which illustrate the effect of pit characteristics and incident wave direction on the water surface elevation.
Criteria for Crack Nucleation in Polycrystalline Ice
Authors: Wu M. S. , Shyam Sunder S.
Published: August 2010

A theoretical analysis of crack nucleation in isotropic polycrystalline ice due to the elastic anisotropy of the constituent crystals has recently been presented by Shyam Sunder and Wu [1]. Subsequently, Shyam Sunder and Nanthikesan [2] have analyzed crack nucleation in polycrystalline ice that is isotropic but porous. The singularity of the stress concentrations near a grain boundary facet junction provides the mechanism for inducing microcrack precursors, if similar nuclei do not already exist. The total stress field is obtained by linearly superposing the microstructural stress field created by the elastic anisotropy mechanism on the applied stress field. Assuming plane stress conditions, the analysis of the nucleation stress is based on a solution to the problem of an extending precursor in a combined stress field including the effects of Coulombic frictional resistance. In the earlier papers, the local material resistance is characterized in terms of a critical value for the maximum principal tensile stress, MPTS, (Erdogan and Sih [3]). This paper compares the nucleation stresses for uniaxial and biaxial loading conditions obtained previously with those obtained from the use of a critical strain energy density, SED, factor (Sih [4]) to characterize the local material resistance. The results, synthesized into biaxial nucleation surfaces, are compared with the limiting tensile strain, LTS, criterion of Shyam Sunder and Ting [5]. The critical precursor orientation and the incipient growth direction for the two models are also compared.
The perceptual organization of sine-wave speech under competitive conditions
Authors: Roberts Brian , Summers Robert J. , Bailey Peter J.
Published: August 2010

Speech comprises dynamic and heterogeneous acoustic elements, yet it is heard as a single perceptual stream even when accompanied by other sounds. The relative contributions of grouping “primitives” and of speech-specific grouping factors to the perceptual coherence of speech are unclear, and the acoustical correlates of the latter remain unspecified. The parametric manipulations possible with simplified speech signals, such as sine-wave analogues, make them attractive stimuli to explore these issues. Given that the factors governing perceptual organization are generally revealed only where competition operates, the second-formant competitor (F2C) paradigm was used, in which the listener must resist competition to optimize recognition [Remez, R. E., et al. (1994). Psychol. Rev. 101, 129–156]. Three-formant (F1+F2+F3) sine-wave analogues were derived from natural sentences and presented dichotically (one ear=F1+F2C+F3; opposite ear=F2). Different versions of F2C were derived from F2 using separate manipulations of its amplitude and frequency contours. F2Cs with time-varying frequency contours were highly effective competitors, regardless of their amplitude characteristics. In contrast, F2Cs with constant frequency contours were completely ineffective. Competitor efficacy was not due to energetic masking of F3 by F2C. These findings indicate that modulation of the frequency, but not the amplitude, contour is critical for across-formant grouping.
On advantages of derivation of exact dynamical stiffness matrices from boundary integral equations
Authors: Søe-Knudsen Alf
Published: August 2010

Dynamical stiffness matrices are broadly used for solving problems in wave propagation in elastic structures. For elastic waveguides that support both propagating and evanescent waves, the standard use of transfer matrices to obtain their dynamical stiffness matrix may cause problems in computations. In this letter to the editor, an advanced way to derive dynamical stiffness matrices is proposed and exemplified in the classical Bernoulli–Euler beam theory.
Experimental observations of active invariance striations in a tank environment
Authors: Quijano Jorge E. , Campbell Richard L. , Oesterlein Tobias G. , Zurk Lisa M.
Published: August 2010

The waveguide invariant in shallow water environments has been widely studied in the context of passive sonar. The invariant provides a relationship between the frequency content of a moving broadband source and the distance to the receiver, and this relationship is not strongly affected by small perturbations in environment parameters such as sound speed or bottom features. Recent experiments in shallow water suggest that a similar range-frequency structure manifested as striations in the spectrogram exists for active sonar, and this property has the potential to enhance the performance of target tracking algorithms. Nevertheless, field experiments with active sonar have not been conclusive on how the invariant is affected by the scattering kernel of the target and the sonar configuration (monostatic vs bistatic). The experimental work presented in this paper addresses those issues by showing the active invariance for known scatterers under controlled conditions of bathymetry, sound speed profile and high SNR. Quantification of the results is achieved by introducing an automatic image processing approach inspired on the Hough transform for extraction of the invariant from spectrograms. Normal mode simulations are shown to be in agreement with the experimental results.
Communication calls of little brown bats display individual-specific characteristics
Authors: Melendez Karla V. , Feng Albert S.
Published: August 2010

Bats’ echolocation signals have been shown to be situation-, colony-, and individual-specific, but whether or not these findings apply to bats’ communication signals is not fully understood. The primary goal of this study was to test the hypothesis that the communication calls of adult little brown bats (Myotis lucifugus) are individual specific. Bats were paired to form focal pairs from June 2007 to August 2008. Each bat’s vocalizations were recorded on a PC-based digital recorder with a custom made ultrasonic microphone. The vocal signals were first classified using a previously established classification scheme. Three acoustic parameters (the minimum and maximum frequencies, and the call duration) of two of the dominant call-types, the steep-FM and broadband noise bursts, of individual bats were further analyzed. Discriminant function analysis, and multi- and univariate analyses of variance of these parameters revealed that these vocal signals were individually distinct and likely contain individual signatures to allow bats to identify individuals acoustically.
On- and off-frequency compression estimated using a new version of the additivity of forward masking technique
Authors: Plack Christopher J. , Arifianto Dhany
Published: August 2010

On- and off-frequency compression at the 4000- and 8000-Hz cochlear places were estimated using a new version of the additivity of forward masking (AFM) technique, that measures the effects of combining two non-overlapping forward maskers. Instead of measuring signal thresholds to estimate compression of the signal as in the original AFM technique, the decrease in masker threshold in the combined-masker condition compared to the individual-masker conditions is used to estimate compression of the masker at the signal place. By varying masker frequency it is possible to estimate off-frequency compression. The maskers were 500-Hz-wide bands of noise, and the signal was a brief pure tone. Compression at different levels was estimated using different overall signal levels, or different masker-signal intervals. It was shown that the new AFM technique and the original AFM technique produce consistent results. Considerable compression was observed for maskers well below the signal frequency, suggesting that the assumption of off-frequency linearity used in other techniques may not be valid. Reducing the duration of the first masker from 200 to 20 ms reduced the compression exponent in some cases, suggesting a possible influence of olivocochlear efferent activity.
Underwater imaging using a hybrid Kirchhoff migration: Direction of arrival method and a sparse surface sensor array
Authors: Dord Jean-Francois , Farhat Charbel
Published: August 2010

This paper considers the problem of imaging a complex object submerged in shallow waters using a sparse surface sensor array and a hybrid signal processing method. This method is constructed by refining the Kirchhoff migration technique to incorporate a zoning of the sensors and an analysis of multiple reflections, and combining it with the direction of arrival estimation method. Its performance is assessed and analyzed with the shape identification of a mockup submarine by numerical simulation. The obtained numerical results highlight the potential of this approach for identifying underwater intruders.
A phase comparison technique for sound velocity measurement in strongly dissipative liquids under pressure
Authors: Khelladi Hassina , Plantier Frédéric , Daridon Jean Luc
Published: August 2010

An accurate technique for the sound velocity measurement in strongly dissipative liquids is elaborated. This technique is based upon high sensitive phase detection. Each medium, at a given temperature and pressure, is characterized by a specific phase shift due to the propagation of the ultrasonic wave within the analyzed medium. By tuning the insonation frequency of the ultrasonic signal, a succession of consecutive nulls of the output dc voltage generated by the phase detector is observed. Thus from the obtained series of frequency values, the sound velocity is computed. Numerous organic liquids, such as alcohols and alkanes, have been used to validate this experimental procedure. As the developed method is well suited for the sound velocity measurement in strongly dissipative liquids, measurements of compressional wave velocity in heavy oil are also carried out over the temperature range 10 °C to 50 °C. The experimental results agree well with those found in the literature. The accuracy of the developed method is estimated at about ±0.3%.
Frequency-dependent and longitudinal changes in noise-induced hearing loss in a bottlenose dolphin (Tursiops truncatus)
Authors: Finneran James J. , Schlundt Carolyn E.
Published: August 2010

Temporary threshold shift (TTS) was measured in a bottlenose dolphin (Tursiops truncatus) after exposure to 16-s tones at 3 and 20 kHz to examine the effects of exposure frequency on the onset and growth of TTS. Thresholds were measured approximately one-half octave above the exposure frequency using a behavioral response paradigm featuring an adaptive staircase procedure. Preliminary data provide evidence of frequency-specific differences in TTS onset and growth, and increased susceptibility to auditory fatigue after exposure to 3-kHz tones compared to data obtained two years earlier.
Auditory frequency focusing is very rapid
Authors: Reeves Adam , Scharf Bertram
Published: August 2010

The present experiments examine the effect of a weak 40-ms tone burst (cue) on the detection of a closely following 40-ms signal at the same frequency. Detection becomes more difficult as the temporal separation (onset to onset) between them shortens from around 300 ms to under 52 ms. The threshold increase or proximal interference is similar whether signal frequency is constant from trial to trial—frequency certainty—or changing—frequency uncertainty. The increase is also similar whether the cue goes to the same ear as the signal or to the opposite ear. This contralateral interference by such weak cues, only 4 dB SL against a continuous broadband noise, appears to exclude a role for forward masking by the cues. When the preceding tone burst differs in frequency from the signal, threshold increases little at any temporal separation. Combined with earlier results on frequency uncertainty (Scharf, B., et al., 2007, J. Acoust. Soc. Am. 121, 2149–2157), the present results show that a listener can shift focusing to an unexpected signal frequency in less than 52 ms. However, the rapidity of focusing is usually obscured by proximal interference, which possibly occurs whenever cue and signal share the same period (∼200 ms) of temporal integration.
A computational study of the effect of vocal-fold asymmetry on phonation
Authors: Xue Q. , Mittal R. , Zheng X. , Bielamowicz S.
Published: August 2010

Unilateral laryngeal paralysis leads to tension imbalance and hence to asynchronous movements between the two vocal folds during phonation. In the current study, a computational model of phonation that couples a two-mass model of the vocal folds with a Navier-Stokes model of the glottal airflow, has been used to examine the dynamics of vocal fold configurations with tension imbalance and its implications for phonation. The simulations show that tension imbalance influences phonation onset, intensity as well as the fundamental phonation frequency. Distinct non-linear effects such as period-doubling bifurcation and preferential frequency selection are also observed.