bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inhomogeneous stability of bacteriorhodopsin in purple membrane against photobleaching at high temperature
Authors: Yokoyama Yasunori , Sonoyama Masashi , Mitaku Shigeki 
Published: January 2004

AbstractHeterogeneity in the state of bacteriorhodopsin in purple membrane was studied through temperature jump experiments carried out in darkness and under illumination with visible light. The thermal denaturation, the irreversible component of spectral change at high temperature, had two decay components, suggesting that bacteriorhodopsin in purple membrane has heterogeneous stability. The temperature dependence of kinetic parameters under illumination revealed that the fast‐decay component gradually increased at above 60°C, indicating that the proportion of unstable bacteriorhodopsin increased. Significant change in the visible circular dichroism (CD) spectra was observed in darkness in the same temperature range as the increase of the fast‐decay component under illumination. Denaturation experiments for C‐terminal‐cleaved bacteriorhodopsin showed that the C‐terminal segment had some effect on the structural stability of bacteriorhodopsin under illumination. Dynamic and static models of the inhomogeneous stability of bacteriorhodopsin in purple membrane are discussed on the basis of the results of the denaturation kinetics and the visible CD spectra. Proteins 2004;54:000–000. © 2004 Wiley‐Liss, Inc.
Functional interaction of 13 yeast SCF complexes with a set of yeast E2 enzymes in vitro
Authors: Kus Bart M. , Caldon Catherine E. , Andorn‐Broza Ronit , Edwards Aled M. 
Published: January 2004

AbstractSCF complexes are multi‐subunit ubiquitin ligases that, in concert with the E1 and E2 ubiquitination enzymes, catalyze the ubiquination of specific target proteins. Only three yeast SCFs have been reconstituted and characterized to date; each of these ubiquitinates its target protein with the E2 Cdc34. We have reconstituted and purified 1 known and 12 novel yeast SCF complexes, and explored the ability of these complexes to function with 5 different purified E2 enzymes; Ubc1, Cdc34, Ubc4, Ubc8 and Ubc11. We have found that the ubiquitination of Sic1 by the reconstituted SCFCdc4 complex was specifically catalyzed by two of the five E2 enzymes tested in vitro; Cdc34 and Ubc4. We also show that at least eight of the purified SCF complexes clearly ubiquitinated their F‐box proteins in vitro, lending support for a regulatory mechanism in which F‐box proteins catalyze their own destruction. The autoubiquitination of each F‐box was in some cases catalyzed only by Cdc34, and in other cases preferentially catalyzed by Ubc4. Ubc4 thus interacts with multiple SCFs in vitro, and the interactions among SCF and E2 components of the ubiquitination machinery may allow further diversification of the roles of SCFs in vivo. Proteins 2004;54:000–000. © 2003 Wiley‐Liss, Inc.
The effects of shortening lactoferrin derived peptides against tumour cells, bacteria and normal human cells
Authors: Yang Nannan , Strøm Morten B. , Mekonnen Seble M. , Svendsen John S. , Rekdal Øystein 
Published: January 2004

AbstractA number of shortened derivatives of the lactoferrin model peptide L12, PAWRKAFRWAKRMLKKAA, were designed in order to elucidate the structural basis for antitumour activity of lactoferrin derivatives. Three tumour cell lines were included in the study and toxicity determined by measuring lysis of human red blood cells and fibroblasts. The results demonstrated a strong correlation between antitumour activity and net positive charge, in which a net charge close to +7 was essential for a high antitumour activity. In order to increase the antitumour activity of the shortest peptide with a net charge less than +7, the hydrophobicity had to be increased by adding a bulky Trp residue. None of the peptides were haemolytic, but toxicity against fibroblasts was observed. However, modifications of the peptides had a higher effect on reducing fibroblast toxicity than antitumour activity and thereby resulted in peptides displaying an almost 7‐fold selectivity for tumour cells compared with fibroblasts. The antimicrobial activity against the Gram‐negative bacteria Escherichia coli and the Gram‐positive bacteria Staphylococcus aureus was also included in order to compare the structural requirements for antitumour activity with those required for a high antimicrobial activity. The results showed that most of the peptides were highly active against both bacterial strains. Less modification by shortening the peptide sequences was tolerated for maintaining a high antitumour activity and selectivity compared with antimicrobial activity. The order of the amino acid residues and thereby the conformation of the peptides was highly essential for antitumour activity, whereas the antimicrobial activity was hardly influenced by changes in this parameter. Thus, in addition to a certain net positive charge and hydrophobicity, the ability to adopt an amphipathic conformation was a more critical structural parameter for antitumour activity than for antimicrobial activity, and implied that a higher flexibility or number of active conformations was tolerated for the peptides to exert a high antimicrobial activity. Copyright © 2003 European Peptide Society and John Wiley & Sons, Ltd.
Expediting the Fmoc solid phase synthesis of long peptides through the application of dimethyloxazolidine dipeptides
Authors: White Peter , Keyte John W. , Bailey Kevin , Bloomberg Graham 
Published: January 2004

AbstractThis paper describes the step‐wise Fmoc solid phase synthesis of a 95‐residue peptide related to FAS death domain. Attempts to prepare this peptide employing conventional amino acid building blocks failed. However, by the judicious use of dimethyloxazolidine dipeptides of serine and threonine, the peptide could be readily prepared in remarkable purity by applying single 1 h coupling reactions. Copyright © 2003 European Peptide Society and John Wiley & Sons, Ltd.
Oligopeptide‐mediated acceleration of amyloid fibril formation of amyloid β(Aβ) and α‐synuclein fragment peptide (NAC)
Authors: Kuroda Yoshihiro , Maeda Yoshitaka , Hanaoka Hirofumi , Miyamoto Kazuhide , Nakagawa Terumichi 
Published: January 2004

AbstractThe effects of oligopeptides on the secondary structures of Aβ and NAC, a fragment of α‐synuclein protein, were studied by circular dichroism (CD) spectra. The effects of oligopeptides on the amyloid fibril formation were also studied by fluorescence spectra due to thioflavine‐T. The oligopeptides were composed of a fragment of Aβ or NAC and were interposed by acidic or basic amino acid residues. The peptide, Ac‐ELVFFAKK‐NH2, which involved a fragment Leu‐Val‐Phe‐Phe‐Ala at Aβ(17–21), had no effect on the secondary structures of Aβ(1–28) in 60% or 90% trifluoroethanol (TFE) solutions at both pH 3.2 and pH 7.2. However, it showed pronounced effects on the secondary structure of Aβ(1–28) at pH 5.4. The Ac‐ELVFFAKK‐NH2 reduced the α‐helical content, while it increased the β‐sheet content of Aβ(1–28). In phosphate buffer solutions at pH 7.0, Ac‐ELVFFAKK‐NH2 had little effect on the secondary structures of Aβ(1–28). However, it accelerated amyloid fibril formation when monitored by fluorescence spectra due to thioflavine‐T. On the other hand, LPFFD, a peptide known as a β‐sheet breaker, caused neither an appreciable extent of change in the secondary structure nor amyloid fibril formation in the same buffer solution. The peptide, Ac‐ETVK‐NH2, which involved a fragment Thr‐Val at NAC(21–22), had no effect on the secondary structure of NAC in 90% TFE and in isotonic phosphate buffer. However, Ac‐ETVK‐NH2 in water with small amounts of NaN3 and hexafluoroisopropanol greatly increased the β‐sheet content of NAC after standing the solution for more than 1 week. Interestingly, in this solution, Ac‐ETVK‐NH2, accelerated the fibril formation of NAC. It was concluded that an oligopeptide that involves a fragment of amyloidogenic proteins could be a trigger for the formation of amyloid plaques of the proteins even when it had little effect on the secondary structures of the proteins as monitored by CD spectra for a short incubation time. Copyright © 2003 European Peptide Society and John Wiley & Sons, Ltd.
Transition state isosteres of the γ‐glutamyl peptide bond hydrolysis: synthesis and characterization of the ψ[CH2NH] pseudopeptide analogue of glutathione
Authors: Cacciatore Ivana , Stefano Antonio Di , Luisi Grazia , Pinnen Francesco , Sozio Piera 
Published: January 2004

AbstractThe fully deprotected glutathione analogue containing the aminomethylene unit as transition state isostere of the γ‐Glu‐Cys peptide bond was synthesized for the first time and characterized in both the reduced and oxidized forms. Copyright © 2003 European Peptide Society and John Wiley & Sons, Ltd.
A contribution to the nomenclature of depsipeptides
Authors: Filip Sorin V. , Cavelier Florine 
Published: January 2004

AbstractDepsipeptides, also called peptolides, are a class of peptidic compounds in which an amide bond has been replaced with an ester bond. The literature does not clearly display rules for the nomenclature of such compounds. Here a method is proposed to transcribe drawn depsipeptide structures in one‐line text. Copyright © 2003 European Peptide Society and John Wiley & Sons, Ltd.
cDNA cloning of the housefly pigment‐dispersing factor (PDF) precursor protein and its peptide comparison among the insect circadian neuropeptides
Authors: Matsushima Ayami , Sato Seiji , Chuman Yoshiro , Takeda Yukimasa , Yokotani Satoru , Nose Takeru , Tominaga Yoshiya , Shimohigashi Miki , Shimohigashi Yasuyuki 
Published: January 2004

AbstractPigment‐dispersing factor (PDF), an 18‐amino acid neuropeptide, is a principal circadian neurotransmitter for the circadian rhythms of the locomotor activity in flies. Recently, two completely different types of PDF precursor were clarified; that of the cricket Gryllus bimaculatus and that of the last‐summer cicada Meimuna opalifera. The G. bimaculatus PDF precursor is extraordinarily short and comprises a nuclear localization signal (NLS), while the M. opalifera PDF precursor is of ordinary length, comparable to that seen for the precursors of crustacean β‐PDH homologues. Although their PDF peptide regions were exactly the same, the regions containing a signal peptide combined with a PDF‐associated peptide (PAP) were remarkably different from each other. Such a grouping suggested a fundamental role for the PAP peptide in the circadian clock, perhaps associated with PDF function. In the present study, the cDNA cloning of PDF from the adult brains of the housefly Musca domestica was carried out and it was found that an isolated clone (527 bp) encodes a PDF precursor protein of ordinary length. The PDF peptide shows a high sequence identity (78%–94%) and similarity (89%–100%) to insect PDFs and also to the crustacean β‐PDH peptides. In particular, there is only a single amino acid difference between the PDFs of Musca and Drosophila; at position 14 Ser for Musca PDF and Asn for Drosophila PDF. A characteristic Ser10 in Drosophila was retained in Musca, indicating the presence of a structural profile unique to these PDFs. The results of sequence analyses suggest that Musca and Drosophila PDFs are to be considered members of a single group that has evolved structurally. When the primary structure of the PAP regions was compared, the Musca PDF precursor also belonged to the same group as that to which the Drosophila PDF precursor belongs. Copyright © 2003 European Peptide Society and John Wiley & Sons, Ltd.
Fluoro‐modified chemotactic peptides: fmlf analogues
Authors: Koksch Beate , Dahl Christina , Radics Gabor , Vocks Andreas , Arnold Klaus , Arnhold Jürgen , Sieler Joachim , Burger Klaus 
Published: January 2004

AbstractA small library of peptide analogues of the chemotactic tripeptide For‐Met‐Leu‐Phe‐NH2 modified by substitution of Leu at position 2 by three different fluorinated amino acids varying in content of fluorine, length of the fluorinated side chain, and alkylation degree at the α‐carbon atom was synthesized. The influence of the fluorine substitution on the biological activity was investigated by measuring the oxidative activity of neutrophils using a luminol‐dependent chemiluminescence assay. Copyright © 2003 European Peptide Society and John Wiley & Sons, Ltd.
The trypsin‐inhibitory, immunostimulatory and antiproliferative activities of a napin‐like polypeptide from Chinese cabbage seeds
Authors: Ng T. B. , Ngai Patrick H. K. 
Published: January 2004

AbstractA heterodimeric 13.8 kDa napin‐like polypeptide has previously been isolated from Chinese cabbage (Brassica parachinensis) seeds with a procedure involving ion exchange chromatography on DEAE‐cellulose, affinity chromatography on Affi‐gel blue gel, FPLC‐ion exchange chromatography on Mono S and FPLC‐gel filtration on Superdex 75. In the present study the N‐terminal sequence of the 8.8 kDa subunit of the polypeptide (PQGPQQRPPKLLQQQTNEEHE) was found to have pronounced homology to napins, albumins and trypsin inhibitors, but demonstrated little similarity to the 5 kDa subunit. The polypeptide stimulated nitrite production by mouse peritoneal macrophages and reduced the viability of leukaemia (L1210) cells. It inhibited trypsin with a higher potency than it inhibited chymotrypsin, but was devoid of ribonuclease and antifungal activities. Copyright © 2003 European Peptide Society and John Wiley & Sons, Ltd.
A Multivariate Analysis on Non‐nucleoside HIV‐1 Reverse Transcriptase Inhibitors and Resistance Induced by Mutation
Authors: Almerico Anna Maria , Lauria Antonino , Tutone Marco , Diana Patrizia , Barraja Paola , Montalbano Alessandra , Cirrincione Girolamo , Dattolo Gaetano 
Published: January 2004

AbstractThis paper describes the use of multivariate statistical procedure PCA as a tool to explore the inhibitory activity of classes of NNRTIs against HIV‐1 viruses (wild type and more frequent mutants, Y181C, V106A, K103N, L100I) and against RT enzyme. The analysis of correlations between biological activity and molecular descriptors or similarity indexes allowed a reliable classification of the fifty five derivatives considered in this study. The best results were obtained in the case of L100I and K103N mutants for which the higher number of assignments was found when the principal components derived from the descriptors were used. On this basis this statistical approach is proposed as a reliable method for the prediction of the activity of NNRTIs, for which the data against mutant strains have not been reported.
Estimation of Carboxylic Acid Ester Hydrolysis Rate Constants
Authors: Hilal S. H. , Karickhoff S. W. , Carreira L. A. , Shrestha B. P. 
Published: January 2004

AbstractSPARC chemical reactivity models were extended to calculate hydrolysis rate constants for carboxylic acid esters from molecular structure. The energy differences between the initial state and the transition state for a molecule of interest are factored into internal and external mechanistic perturbation components. The internal perturbations quantify the interactions of the appended perturber (P) with the reaction center (C). These internal perturbations are factored into SPARC's mechanistic components of electrostatic and resonance effects. External perturbations quantify the solute‐solvent interactions and are factored into H‐bonding, field stabilization and steric effects. These models have been tested using 1471 measured hydrolysis rate constants in water and mixed‐solvent systems at different temperatures. The aggregate RMS deviation of the calculated versus observed values was 0.374 M−1s−1; close to the intralaboratory experimental error.
Analysis of water solubility data on the basis of HYBOT descriptors
Authors: Schaper Klaus‐J. , Kunz Brigitte , Raevsky Oleg A. 
Published: January 2004

AbstractSolubility data of 787 organic liquids (electrolytes and non‐electrolytes) with diverse structures has been quantitatively described by physicochemical property descriptors. Special effects like intra‐ and intermolecular hydrogen bonds have been shown to be very important for water solubility. It is found that an important part of the solute‐solvent interaction is neglected in all correlations of logS with (only) logP, as in this case the solute H‐bond donor effect is not considered. As expected intramolecular hydrogen bonds lead to reduced solubility, whereas intermolecular hydrogen bonds (both HB donors and acceptors) of solutes result in higher solubility. An exception to the latter rule are carboxylic acids which due to intermolecular HB‐induced dimerization in the pure liquid phase of acids show a three times lower solubility as expected on the basis of their molecular properties. A volume‐related term (molecular polarizability α) was found to have an essential negative contribution to solubility. For the first time the solubility increasing effect of partial ionization of weak acids and bases in saturated aqueous solutions has been quantitatively considered for sets of compounds by exact calculation of the pH determined by the solutes aqueous solubility and pKa value(s).
Analysis of water solubility data on the basis of HYBOT descriptors.
Authors: Raevsky Oleg A. , Schaper Klaus‐J. 
Published: January 2004

AbstractThis work describes the analysis of water‐gas phase partitioning data Lw=Cw/Cgfor 559 organic chemicals on the basis of physicochemical descriptors calculated by the HYBOT program package. Physicochemical descriptors combined with indicator variables as well as a new approach combining traditional QSAR and molecular similarity are used to take structural features into account. The H‐bond acceptor ability of chemicals (i.e. interaction of acceptor atoms with hydrogen atoms of water) is the main factor that influences the partitioning of vapors into water. The simultaneous consideration of H‐bond acceptor and donor factors leads to a description of the solubility of vapors with a correlation coefficient of about 0.92. The influence of steric interactions of solutes (characterized by means of molecular polarizability) with water molecules contributes slightly but significantly from the statistics point of view. The use of a set of indicator variables for hydrocarbons and for molecules containing amino, amido, CX3, ether and nitro groups as well as for molecules with ability to form intramolecular hydrogen bonds improves the correlation and helps to take structural features into account. Furthermore, the application of an approach based on the calculation of additional contributions to solubility by considering ‘nearest neighbor chemicals’ and their difference in physicochemical parameters gives in many cases good results and could be very useful in the analysis of vast data sets.
Validation of Poisson‐Boltzmann Electrostatic Potential Fields in 3D QSAR: A CoMFA Study on Multiple Datasets
Authors: Kellogg Glen E. , Phatak Sharangdhar , Nicholls Anthony , Grant J. Andrew 
Published: January 2004

AbstractA CoMFA 3D QSAR (Quantitative Structure‐Activity Relationships) study was performed on five diverse data sets that have been previously published or are otherwise generally available to assess the value of the ZAP electrostatic potential field (calculated from a solution of the Poisson‐Boltzmann Equation) as compared to the Coulombic field as implemented in standard CoMFA. The ZAP field showed an average improvement of 0.114 in q2 (leave‐one‐out cross‐validation) as compared to the Coulombic field, and the steric/ZAP combination field showed an improvement of 0.128 in q2 as compared to the Both (steric and electrostatic) field combination of CoMFA. However, the enhancement is not monolithic – some of the data sets in this study showed a much larger preference for the ZAP field than others. The ZAP field appears to be more physically realistic than the Coulombic field and should be of significant value in QSAR studies of some data sets.
Quantum Chemical‐QSAR Study of Some Newly Synthesized 1,4‐Dihydropyridine Calcium Channel Blockers
Authors: Safarpour M. A. , Hemmateenejad B. , Miri R. , Jamali M. 
Published: January 2004

AbstractA QSAR analysis was conducted on the calcium channel antagonist activity of 72 C‐3 and C‐5 ester‐substituted 4‐(nitro imidazolyl) 1,4‐dihydropyridine derivatives. Quantum chemical descriptors including atomic charges, electrostatic potentials, HOMO and LUMO energies, electronegativity, electrophilicity, hardness and softness indices were calculated using ab‐initio method with gaussian98 at RHF/6‐21G level. Multiple linear regression was used to model the relationships between molecular descriptors and biological activity of molecules using genetic algorithm as variable selection tool (GA‐MLR). A high quality multi‐parametric QSAR model was obtained. The prediction ability of the resulting models was evaluated by the prediction of the activity of the prediction set compounds, which did not contribute to the model building at all. Addition of the physicochemical parameters to the electronic features of the molecules enhanced the prediction ability of the models. Artificial neural network, combined with genetic algorithm for feature selection (GA‐ANN), was also employed to model nonlinear structure‐activity relationships. The results showed that ANN gave more appropriate QSAR models in comparison with those obtained by MLR. The root mean square error of prediction for the best MLR and ANN models, which used 6 descriptors as predictor variables, was equal to 0.60 and 0.21, respectively. Also, the squared correlation coefficient of these models was 0.874 and 0.988, respectively.
Satellite communications: the contribution of the 5th framework programme and future perspectives
Authors: Barani Bernard 
Published: January 2004

AbstractThe telecommunication sector is of key importance for the European economy. Digitization, secure broadband access and mobility are expected to shift an ever‐growing proportion of the economy on line, thus creating new markets and business opportunities. With the eEurope 2002 and eEurope 2005 initiatives, the European Union has initiated a number of policy actions aiming at favouring the rapid introduction of innovative communication systems, services and applications. Research and development, as supported under the IST programme of the Union, is closely associated to the overall policy picture. The IST programme is notably instrumental in supporting, with a longer‐term approach, key policy orientations such as the pervasive introduction of low cost broadband access, introduction of advanced mobile systems, or migration of networks towards the next generation of Internet protocol, IPv6. Satellite communication form an integral part of this diversified communication landscape, and has also been significantly supported under the 5th Framework Programme. Even if the problematic of the satcom industry are to some extent similar to those of the terrestrial players (e.g. catalysing take up of broadband and advanced mobile markets), the strategies followed by the satcom sector differ from those followed by the terrestrial players. This paper review the current technological approaches of the satcom industry, their relevance in the context of the policy goals of the Union, and how they have been supported under the IST programme. It also introduces briefly how co‐ordination with ESA work has been achieved, and the perspectives for further support, notably under the now starting 6th Framework Programme. Copyright © 2004 John Wiley & Sons, Ltd.