bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mechanical force analysis of peptide interactions using atomic force microscopy
Authors: Nakamura Chikashi , Takeda Seiji , Kageshima Masami , Ito Miyuki , Sugimoto Naoki , Sekizawa Kazuko , Miyake Jun 
Published: February 2004

AbstractSome peptides have previously been reported to bind low molecular weight chemicals. One such peptide with the amino acid sequence His–Ala–Ser–Tyr–Ser was selectively screened from a phage library and bound to a cationic porphyrin, 5,10,15,20‐tetrakis(N‐methylpyridinium‐4‐yl)‐21H,23H‐porphine (TMpyP), with a binding constant of 105M−1(J. Kawakami, T. Kitano, and N. Sugimoto, Chemical Communications, 1999, pp. 1765–1766). The proposed binding was due to π‐electron stacking from two aromatic amino acids of histidine and tyrosine. In this study, the weak interactions between TMpyP and the peptide were further investigated by force curve analysis using atomic force microscopy (AFM). The mechanical force required to unbind the peptide–porphyrin complex was measured by vertical movement of the AFM tip. Peptide self‐assembled monolayers were formed on both a gold‐coated mica substrate and a gold‐coated AFM tip. The TMpyPs could bind between the two peptide layers when the peptide‐immobilized AFM tip contacted the peptide‐immobilized substrate in solution containing TMpyP. In the retracting process a force that ruptured the interaction between TMpyPs and peptides was observed. The unbinding force values correlated to the concentration of TMpyP. A detection limit of 100 ng/mL porphyrin was obtained for the force measurement, and was similar to surface plasmon resonance sensor detection limits. Furthermore, we calculated the product of the observed force and the length of the molecular elongation to determine the work required to unbind the complexes. The obtained values of unbinding work were in a reasonable range compared to the binding energy of porphyrin–peptide. © 2004 Wiley Periodicals, Inc. Biopolymers (Pept Sci) , 2004
On selectivity and sensitivity of synthetic multifunctional pores as enzyme sensors: Discrimination between ATP and ADP and comparison with biological pores
Authors: Sordé Nathalie , Matile Stefan 
Published: February 2004

AbstractThis report delineates scope and limitation of the selectivity of synthetic multifunctional pores as enzyme sensors using glycolytic enzymes as example (G. Das, P. Talukdar, and S. Matile, Science, 2002, Vol. 298, pp. 1600–1602). Unproblematic detectability of hexokinase and phosphofructokinase demonstrates that the selectivity of synthetic multifunctional pore (SMPs) sensors suffices to sense ATP in mixed analytes containing ADP, whereas detection of the isomerization of glucose 6‐phosphate into fructose 6‐phosphate by phosphoglucose isomerase is not possible with confidence. The sensitivity of SMP sensors is sufficient for end‐point detection of one picomole poly‐L‐glutamate hydrolyzed by papain in unoptimized assay format; the sensitivity of melittin as representative biological pore of similar charge and aggregation number to detect the same reaction is more than four orders of magnitude inferior. © 2004 Wiley Periodicals, Inc. Biopolymers (Pept Sci) , 2004
Incorporation of thioether building blocks into an αvβ3‐specific RGD peptide: Synthesis and biological activity
Authors: Kelleman Audrey , Mattern Ralph‐Heiko , Pierschbacher Michael D. , Goodman Murray 
Published: February 2004

AbstractWe report the design, synthesis, and binding affinities of a family of thioether analogues of the αvβ3‐specific compound c[(Mpa)RGDD(tBuG)C]‐NH2. The synthesis of the thioether building blocks is scalable and produced the desired products in good yields. The linear peptides were synthesized on solid supports, followed by cyclization in solution. Our analogues demonstrate interesting binding data to the isolated receptors. In particular, the peptide c[NH‐Arg‐Gly‐Asp‐Asp‐(tBuG)‐Cys(S‐CH2‐CO)]NH2 (1) exhibits differences in binding when compared to the parent compound and demonstrates potent affinity to the αvβ3 and α5β1 receptors while having reduced binding to the αIIbβ3 receptor. This result combined with the replacement of the disulfide with a thioether makes this compound interesting for further development. © 2003 Wiley Periodicals, Inc. Biopolymers (Pept Sci), 2003
Design and synthesis of substrate‐based inhibitors of botulinum neurotoxin type B metalloprotease
Authors: Oost Thorsten , Sukonpan Chanokporn , Brewer Matthias , Goodnough Michael , Tepp William , Johnson Eric A. , Rich Daniel H. 
Published: February 2004

AbstractBotulinum toxin (BoNT) metalloproteases and related proteases are the most selective proteases known. X‐ray crystal structures suggest that the native enzymes exist in catalytically incompetent forms that must be activated by substrate binding. In order to characterize the postulated substrate‐induced conformational changes, we synthesized a series of transition state analog inhibitors (TSI) in which the dipeptide cleavage site has been replaced by tetrahedral intermediate analogs within the minimal substrate peptide sequence. Reduced amide, α‐hydroxyamide, α‐thio‐amide, and hydroxyethylamine analogs of —Gln–Phe— were incorporated via solid phase peptide synthesis into 35‐mer analogs of the minimal peptide substrate sequence. The synthesis, characterization, and inhibition kinetics for four series of compounds against holotoxin BoNT/B is described. The α‐thiol amide derivatives of the 35‐mer substrate were found to inhibit BONT/B in the low micromolar range. © 2003 Wiley Periodicals, Inc. Biopolymers (Pept Sci), 2003
1,1,1,3,3,3‐hexafluoroisopropanol induced thermal unfolding and molten globule state of bovine α‐lactalbumin: Calorimetric and spectroscopic studies
Authors: Kundu Agnita , Kishore Nand 
Published: February 2004

AbstractThe thermal denaturation of α‐lactalbumin was studied at pH 7.0 and 9.0 in aqueous 1,1,1,3,3,3‐hexafluoroisopropanol (HFIP) by high‐sensitivity differential scanning calorimetry. The conformation of the protein was analyzed by a combination of fluorescence and circular dichroism measurements. The most obvious effect of HFIP was lowering of the transition temperature with an increase in the concentration of the alcohol up to 0.30M, beyond which no calorimetric transition was observed. Up to 0.30M HFIP the calorimetric and van't Hoff enthalpy remained the same, indicating the validity of the two‐state approximation for the thermal unfolding of α‐lactalbumin. The quantitative thermodynamic parameters accompanying the thermal transitions have been evaluated. Spectroscopic observations confirm that α‐lactalbumin is in the molten globule state in the presence of 0.50M HFIP at pH 7.0 and 0.75M HFIP at pH 9.0. The results also demonstrate that α‐lactalbumin in the molten globule state undergoes a noncooperative thermal transition to the denatured state. It is observed that two of four tryptophans are exposed to the solvent in the HFIP induced molten globule state of α‐lactalbumin compared to four in the 8.5M urea induced denatured state of the protein. It is also observed that the HFIP induced molten globule states at the two pH values are different from the acid induced molten globule state (A state) of α‐lactalbumin. © 2004 Wiley Periodicals, Inc. Biopolymers, 2004
Cloning, expression and characterization of recombinant sweet‐protein thaumatin II using the methylotrophic yeast Pichia pastoris
Authors: Masuda Tetsuya , Tamaki Shinobu , Kaneko Ryosuke , Wada Ritsuko , Fujita Yuki , Mehta Alka , Kitabatake Naofumi 
Published: February 2004

AbstractThaumatin, an intensely sweet‐tasting protein, was secreted by the methylotrophic yeast Pichia pastoris. The mature thaumatin II gene was directly cloned from Taq polymerase‐amplified PCR products by using TA cloning methods and fused the pPIC9K expression vector that contains Saccharomyces cerevisiae prepro α‐mating factor secretion signal. Several additional amino acid residues were introduced at both the N‐ and C‐terminal ends by genetic modification to investigate the role of the terminal end region for elicitation of sweetness in the thaumatin molecule. The secondary and tertiary structures of purified recombinant thaumatin were almost identical to those of the plant thaumatin molecule. Recombinant thaumatin II elicited a sweet taste as native plant thaumatin II; its threshold value of sweetness to humans was around 50 nM, which is the same as that of plant thaumatin II. These results demonstrate that the functional expression of thaumatin II was attained by Pichia pastoris systems and that the N‐ and C‐terminal regions of the thaumatin II molecule do not ‐play an important role in eliciting the sweet taste of thaumatin. © 2004 Wiley Periodicals, Inc.
Yeast plasma membrane Ena1p ATPase alters alkali‐cation homeostasis and confers increased salt tolerance in tobacco cultured cells
Authors: Nakayama Hideki , Yoshida Kazuya , Shinmyo Atsuhiko 
Published: February 2004

AbstractIn plants, the plasma membrane Na+/H+ antiporter is the only key enzyme that extrudes cytosolic Na+ and contributes to salt tolerance. But in fungi, the plasma membrane Na+/H+ antiporter and Na+‐ATPase are known to be key enzymes for salt tolerance. Saccharomyces cerevisiae Ena1p ATPase encoded by the ENA1/PMR2A gene is primarily responsible for Na+ and Li+ efflux across the plasma membrane during salt stress and for K+ efflux at high pH and high K+. To test if the yeast ATPase would improve salt tolerance in plants, we expressed a triple hemagglutinin (HA)‐tagged Ena1p (Ena1p‐3HA) in cultured tobacco (Nicotiana tabacum L.) cv Bright Yellow 2 (BY2) cells. The Ena1p‐3HA proteins were correctly localized to the plasma membrane of transgenic BY2 cells and conferred increased NaCl and LiCl tolerance to the cells. Under moderate salt stress conditions, the Ena1p‐3HA‐expressing BY2 clones accumulated lower levels of Na+ and Li+ than nonexpressing BY2 clones. Moreover, the Ena1p‐3HA expressing BY2 clones accumulated lower levels of K+ than nonexpressing cells under no‐stress conditions. These results suggest that the yeast Ena1p can also function as an alkali‐cation (Na+, Li+, and K+) ATPase and alter alkali‐cation homeostasis in plant cells. We conclude that, even with K+‐ATPase activity, Na+‐ATPase activity of the yeast Ena1p confers increased salt tolerance to plant cells during salt stress. © 2004 Wiley Periodicals, Inc.
Making sense of male rape: constructions of gender, sexuality and experience of rape victims
Authors: Doherty Kathy , Anderson Irina 
Published: February 2004

AbstractThis study reports a preliminary investigation into accounting practices for male rape in conversation. Thirty men and women, in dyads, were asked to discuss an incident of male rape presented to them in a vignette. The findings showed that two main issues were discussed: the experience of the rape act and societal responses to male victims. In addition, participants established a ‘hierarchy of suffering’, where rape was judged to be worse for ‘heterosexual’ men than it is for ‘women’ or ‘gay’ men. Hegemonic, phallocentric representations of heterosexuality were mobilized to argue that acts of rape and consensual intercourse are the same for ‘gay’ men and ‘women’ and therefore less traumatic than for ‘heterosexual’ men. This obscures the violence of rape for gay men and women and exonerates perpetrators by minimizing injury sustained. Participants also argued that heterosexual victims are likely to experience ridicule for having departed from hegemonic masculinity. Arguments were constructed to avoid charges of being dismissive towards women and gay men and of victim blaming in relation to heterosexual men. Copyright © 2004 John Wiley & Sons, Ltd.
Gold Glyconanoparticles as New Tools in Antiadhesive Therapy
Authors: Rojo Javier , Díaz Vicente , de la Fuente Jesús M. , Segura Inmaculada , Barrientos Africa G. , Riese Hans H. , Bernad Antonio , Penadés Soledad 
Published: February 2004

AbstractGold glyconanoparticles (GNPs) have been prepared as new multivalent tools that mimic glycosphingolipids on the cell surface. GNPs are highly soluble under physiological conditions, stable against enzymatic degradation and nontoxic. Thereby GNPs open up a novel promising multivalent platform for biological applications. It has recently been demonstrated that specific tumor‐associated carbohydrate antigens (glycosphingolipids and glycoproteins) are involved in the initial step of tumor spreading. A mouse melanoma model was selected to test glyconanoparticles as possible inhibitors of experimental lung metastasis. A carbohydrate–carbohydrate interaction is proposed as the first recognition step for this process. Glyconanoparticles presenting lactose (lacto‐GNPs) have been used successfully to significantly reduce the progression of experimental metastasis. This result shows for the first time a clear biological effect of lacto‐GNPs, demonstrating the potential application of this glyconanotechnology in biological processes.
Sequence‐specific Methyltransferase‐Induced Labeling of DNA (SMILing DNA)
Authors: Pljevaljčić Goran , Schmidt Falk , Weinhold Elmar 
Published: February 2004

AbstractA new concept for sequence‐specific labeling of DNA by using chemically modified cofactors for DNA methyltransferases is presented. Replacement of the amino acid side chain of the natural cofactor S‐adenosyl‐L‐methionine with an aziridine group leads to a cofactor suitable for DNA methyltransferase‐catalyzed sequence‐specific coupling with DNA. Sequence‐specifically fluorescently labeled plasmid DNA was obtained by using the DNA methyltransferase from Thermus aquaticus (M.TaqI) as catalyst and attaching a fluorophore to the aziridine cofactor. First results suggest that all classes of DNA methyltransferases with different recognition sequences can be used. In addition, this novel method for DNA labeling should be applicable to a wide variety of reporter groups.
A Proposed Mechanism for the Reductive Ring Opening of the Cyclodiphosphate MEcPP, a Crucial Transformation in the New DXP/MEP Pathway to Isoprenoids Based on Modeling Studies and Feeding Experiments
Authors: Brandt Wolfgang , Dessoy Marco A. , Fulhorst Michael , Gao Wenyun , Zenk Meinhart H. , Wessjohann Ludger A. 
Published: February 2004

AbstractExperimental and theoretical investigations concerning the second‐to‐last step of the DXP/MEP pathway in isoprenoid biosynthesis in plants are reported. The proposed intrinsic or late intermediates 4‐oxo‐DMAPP (12) and 4‐hydroxy‐DMAPP (11) were synthesized in deuterium‐ or tritium‐labeled form according to new protocols especially adapted to work without protection of the diphosphate moiety. When the labeled compounds MEcPP (7), 11, and 12 were applied to chromoplast cultures, aldehyde 12 was not incorporated. This finding is in agreement with a mechanistic and structural model of the responsible enzyme family: a three‐dimensional model of the fragment L271–A375 of the enzyme GcpE of Streptomyces coelicolor including NADPH, the Fe4S4 cluster, and MEcPP (7) as ligand has been developed based on homology modeling techniques. The model has been accepted by the Protein Data Bank (entry code 1OX2). Supported by this model, semiempirical PM3 calculations were performed to analyze the likely catalysis mechanism of the reductive ring opening of MEcPP (7), hydroxyl abstraction, and formation of HMBPP (8). The mechanism is characterized by a proton transfer (presumably from a conserved arginine 286) to the substrate, accompanied by a ring opening without high energy barriers, followed by the transfer of two electrons delivered from the Fe4S4 cluster, and finally proton transfer from a carboxylic acid side chain to the hydroxyl group to be removed from the ligand as water. The proposed mechanism is in agreement with all known experimental findings and the arrangement of the ligand within the enzyme. Thus, a very likely mechanism for the second to last step of the DXP/MEP pathway in isoprenoid biosynthesis in plants is presented. A principally similar mechanism is also expected for the reductive dehydroxylation of HMBPP (8) to IPP (9) and DMAPP (10) in the last step.
Structure–Activity Studies on the Corticotropin Releasing Factor Antagonist Astressin, leading to a Minimal Sequence necessary for Antagonistic Activity
Authors: Rijkers Dirk T. S. , Kruijtzer John A. W. , van Oostenbrugge Marja , Ronken Eric , den Hartog Jack A. J. , Liskamp Rob M. J. 
Published: February 2004

AbstractCorticotropin Releasing Factor (CRF) antagonists are considered promising for treatment of stress‐related illnesses such as major depression and anxiety‐related disorders. We report here the design, synthesis and biological evaluation of 91 truncated astressin analogues in order to deduce the pharmacophoric amino acid residues. Such truncated peptides may serve as valuable lead structures for the development of new small, non‐peptide‐based CRF antagonists. N‐Terminal truncation of astressin led to active CRF antagonists that are substantially reduced in size and are selectively active at the human CRF receptor type 1 in vitro and in vivo. Subsequently, an alanine scan in combination with further truncated derivatives led to the proposal of a new pharmacophoric model of peptide‐based CRF antagonists. It was found that the astressin(27–41)C sequence is the shortest active CRF antagonist. The first eight N‐terminal amino acid residues were found to be an important structural determinant and were replaceable by alanine residues, thus enhancing the α‐helical propensity. A covalent structural constraint is of utmost importance for the preorganization of the C‐terminal amino acid residues. The C‐terminal heptapeptide sequence, however, was found to be crucial for the antagonistic activity, since substitution or deletion of any residue led to inactive compounds.
DNA Compaction by Divalent Cations: Structural Specificity Revealed by the Potentiality of Designed Quaternary Diammonium Salts
Authors: Zinchenko Anatoly A. , Sergeyev Vladimir G. , Yamabe Kuniaki , Murata Shizuaki , Yoshikawa Kenichi 
Published: February 2004

AbstractDNA interaction with quaternary diammonium dications, R(CH3)2N+(CH2)nN+(CH3)2R, having various intercharge distances, lengths, and branching, and the chemical nature of the hydrophobic substituents were investigated by fluorescent microscopy and circular dichroism (CD) spectroscopy to reveal their structural specificity for binding to DNA. The conformational behavior of DNA was found to be highly sensitive to the structure of the dications with separated charges. The distance between two ammonium groups greatly influences the compaction activity of the dications. To explain this situation, we proposed a model that demonstrates that the charge density of the dication and the geometric fit between DNA phosphates and the ammonium groups in the dications play an important role in providing efficient DNA collapse. Elongation of the alkyl substituents (R) in the diammonium salts from ethyl to hexyl did not generate any significant alterations in the compaction activities, whereas the branching of substituents caused a drastic decrease in their compaction ability. Based on the results of CD spectroscopy, it was found that the ability of the dications to provoke a DNA transition from the B‐form to A‐form was also specific: it depended on their intercharge distances and was independent of the length of alkyl substituents.
LDA‐Measurements in a Stirred Tank With a Liquid‐Liquid System at High Volume Percentage Dispersed Phase
Authors: Svensson F.J.E. , Rasmuson A. 
Published: February 2004

AbstractThe purpose of this study is to evaluate how the flow is influenced by the volume percentage of dispersed phase in a liquid‐liquid system. A novel model system consisting of two refraction index matched immiscible liquids is presented along with experimental velocity vector fields of the continuous phase that utilises the non‐intrusive Laser‐Doppler‐Anemometry technique. Three velocity components have been measured inside a baffled cylindrical tank, stirred with a six‐bladed Rushton‐impeller. The experiments show that the vortex below the impeller is stretched, primarily in the radial direction, with increasing dispersed phase content. A small change in the shape of the vortex above the impeller can also be observed. The turbulence is dampened with increasing dispersed volume fraction.
Mixing Studies Related to the Cleaning of Molten Aluminium
Authors: Kimata M. , Nayan N. , Bujalski W. , Nienow Alvin W. , Song J.L. , Jolly M.R. 
Published: February 2004

AbstractMolten aluminium is traditionally “cleaned” by a chlorine‐based fluxing gas. This gas also has to provide the motive power for mixing. Recently, mechanical agitation with solid fluxes has been considered as a replacement for environmental reasons. Here, these two methods of mixing are compared using particle image velocimetry (PIV), decolourisation for homogenisation and power measurement for comparison of efficiencies. A geometrically scaled‐down vessel was used, with air to mimic “chlorine” fluxing and with water as the working fluid. At equivalent mean specific energy dissipation rates, $ \bar \varepsilon $T, maximum velocities are higher and mixing times are shorter with an impeller. This improved performance is achieved with the impeller without causing surface gas entrainment, the latter being detrimental to fluxing.
CFD Modeling of Turbulent Jacket Heat Transfer in a Rushton Turbine Stirred Vessel
Authors: Zakrzewska B. , Jaworski Z. 
Published: February 2004

AbstractCFD modelling of the turbulent heat transfer was performed for a stirred tank equipped with a Rushton turbine impeller and four standard baffles. Eight different turbulence models, i.e. the standard k‐ϵ, RNG k‐ϵ, realizable k‐ϵ, Chen‐Kim k‐ϵ, optimized Chen‐Kim k‐ϵ, standard k‐ω, k‐ω SST and Reynolds stress models, were used during the modelling. In all investigated cases, the boundary flow at the vessel wall was described by the standard logarithmic wall functions. The CFD modelling values of the local heat transfer coefficient were compared with the corresponding experimental data. The best agreement was obtained for the standard k‐ϵ, optimized Chen‐Kim k‐ϵ and k‐ω SST models.
Gas Flow Behavior in a Two‐Phase Reactor Stirred with Triple Turbines
Authors: Majirova H. , Pinelli D. , Machon V. , Magelli F. 
Published: February 2004

AbstractGas behavior was studied in a gas‐liquid reactor stirred with multiple turbines. Triple PBTs pumping either down or up and BT‐6's were used. The behavior of coalescing (water) and non‐coalescing (sodium sulfate solution) systems was investigated. The gas phase behavior was characterized by means of the RTD and modeled with the axial dispersion model. This model was confirmed to interpret the experimental data well for water and satisfactorily for the coalescence‐inhibiting solutions. The influence of the operating conditions, turbine type and system coalescing behavior on the model parameters is discussed. Comparison is also made with similar data regarding Rushton turbines and high‐solidity ratio hydrofoils, as well as gas holdup.
Design of Horizontal Vessels Operated as CSTR – Basic Mixing Tasks, RTD, Productivity
Authors: Forschner P. , Houlton D. , Kassera V. , Klepper R. , Krebs R. 
Published: February 2004

AbstractAgitator performance in standard vertical vessels with cylindrical shape, dished bottom and zero to four baffles has been the topic of numerous publications. In certain industries, however, horizontal cylindrical vessels with hemispherical ends, divided internally into multiple compartments, are preferred for continuous processes operating at high pressures. Use of standard correlations derived from vertical vessels may lead to incorrect performance predictions for these horizontal vessels, and hence unsatisfactory process results. A number of laboratory trials were undertaken to identify differences in behavior and potential means to improve design for horizontal vessels. Differences with respect to solids suspension, mixing time and residence time distribution were studied. CFD simulations were undertaken and validated against the experimental results.