bluuebunny/crossref_metadata_2025 huggingface dataset:
Fluorescent probes for monitoring the pulsed‐laser‐induced photocuring of poly(urethane acrylate)‐based adhesives
Authors: Peinado Carmen , Salvador Enrique F. , Corrales Teresa , Bosch Paula , Catalina Fernando
Published: January 2004

Fluorescence spectroscopy was used to study the kinetics of polymerization of acrylic adhesive formulations exposed to a 355‐nm pulsed emission from an Nd‐YAG laser. Nine fluorescent probes were used for monitoring the laser curing, showing different sensitivities. In general, the fluorescence intensity emission increased as crosslinking occurred. In addition, solvatochromic fluorescent probes showed a blueshift in their emission. A relative method was applied for the evaluation of the polymerization rates in three different acrylic systems. Special features of pulsed‐laser‐induced polymerization were treated in detail, such as the influence of the laser pulse frequency and the incident laser beam intensity. The polymerization rate slowed down as the pulse repetition rate decreased. An inhibition period due to oxygen quenching was observed, and it was highly dependent on the laser repetition rate and the nature of the photoinitiator. The effect of the laser beam intensity on the kinetics of such fast reactions was studied. In general, increasing the laser energy improved the rate of polymerization. The degree of cure improved as the polymerization rate increased as a result of faster crosslinking, rather than relaxation volume kinetics. Moreover, a saturation rate effect occurred that depended on the photoinitiator. The different behaviors of the two photoinitiators in the curing of the same acrylic formulation was explained on the basis of primary radical termination. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 1227–1238, 2004
Measurement of the dissolved oxygen concentration in acrylate monomers with a novel photochemical method
Authors: Gou Lijing , Coretsopoulos Chris N. , Scranton Alec B.
Published: January 2004

Because of the well‐known radical‐scavenging behavior, molecular oxygen is capable of inhibiting free‐radical chain polymerizations of unsaturated monomers. The deleterious effects of diffused oxygen in a polymerization system result in both a reduced polymerization rate and the loss of surface properties of a polymer film or coating. However, reliable data for oxygen concentration in organic monomers are relatively scarce because of the experimental and instrumental limitations of the commercially available techniques. In this study, a photochemical method was developed and was used to obtain the dissolved oxygen concentration in seven acrylate monomers. The principle of the method was to convert ground‐state molecular oxygen dissolved in monomer to the excited, singlet‐state oxygen and then react the singlet oxygen with a third compound (singlet oxygen trapper). By monitoring the concentration of this singlet oxygen trapper spectrophotometrically, the concentration of dissolved oxygen can be obtained with the established stoichiometry for the reaction between singlet oxygen and trapper. The singlet oxygen concentrations in the acrylate monomers varied from 0.59 to 2.07 × 10−3 mol/L, depending on the monomer structure. The strategies and considerations for generalizing the method to other systems, including highly oxygenated organics, are discussed. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 1285–1292, 2004
Copper‐mediated radical polymerization on a microcellular monolith surface
Authors: Moine Laurence , Deleuze Hervé , Degueil Marie , Maillard Bernard
Published: January 2004

High‐capacity microcellular monoliths were prepared by a two‐step process, including the synthesis of a bromoester‐functionalized scaffold by the copolymerization of a highly concentrated emulsion and an in situ surface polymerization of methyl methacrylate with atom transfer radical polymerization. The influence of various parameters, such as the feed ratio, the concentration of immobilized bromoester groups, and the presence of a spacer group on the poly(methyl methacrylate) loading, was studied. Monoliths with capacities of up to 7 mmol g−1 were obtained. Thermogravimetric analyses, scanning electron microscopy experiments, and mercury intrusion porosimetry measurements were used for the characterization of the final materials. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 1216–1226, 2004
Preparation and properties of poly(N‐isopropylacrylamide)/poly(N‐isopropylacrylamide) interpenetrating polymer networks for drug delivery
Authors: Zhang Jian‐Tao , Huang Shi‐Wen , Cheng Si‐Xue , Zhuo Ren‐Xi
Published: January 2004

A novel poly(N‐isopropylacrylamide) (PNIPA)/PNIPA interpenetrating polymer network (IPN) was synthesized and characterized. In comparison with conventional PNIPA hydrogels, the shrinking rate of the IPN hydrogel increased when gels, swollen at 20 °C, were immersed in 50 °C water. The phase‐transition temperature of the IPN gel remained unchangeable because of the same chemical constituent in the PNIPA gel. The reswelling kinetics were slower than those of the PNIPA hydrogel because of the higher crosslinking density of the IPN hydrogel. The IPN hydrogel had better mechanical strength because of its higher crosslinking density and polymer volume fraction. The release behavior of 5‐fluorouracil (5‐Fu) from the IPN hydrogel showed that, at a lower temperature, the release of 5‐Fu was controlled by the diffusion of water molecules in the gel network. At a higher temperature, 5‐Fu inside the gel could not diffuse into the medium after a burst release caused by the release of the drug on the surface of the gel. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 1249–1254, 2004
Poly(phenylene vinylene)‐based copolymers containing 3,7‐phenothiazylene and 2,6‐pyridylene chromophores: Fluorescence sensors for acids, metal ions, and oxidation
Authors: Wu Tzi‐Yi , Chen Yun
Published: January 2004

A novel copolymer, poly(N‐hexyl‐3,7‐phenothiazylene‐1,2‐ethenylene‐2,6‐pyridylene‐1,2‐ethenylene) (P3), containing N‐hexyl‐3,7‐phenothiazylene and 2,6‐pyridylene chromophores was synthesized to investigate the effect of protonation, metal complexation, and chemical oxidation on its absorption and photoluminescence (PL). Poly(N‐hexyl‐3,8‐iminodibenzyl‐1,2‐ethenylene‐1,3‐phenylene‐1,2‐ethenylene) and poly(N‐hexyl‐3,7‐phenothiazylene‐1,2‐ethenylene‐1,3‐phenylene‐1,2‐ethenylene) (P2), consisting of 1,3‐divinylbenzene alternated with N‐hexyl‐3,8‐iminodibenzyl and N‐hexyl‐3,7‐phenothiazylene, respectively, were also prepared for comparison. Electrochemical investigations revealed that P3 exhibited lower band gaps (2.34 eV) due to alternating donor and acceptor conjugated units (push–pull structure). The absorption and PL spectral variations of P3 were easily manipulated by protonation, metal chelation, and chemical oxidation. P3 displayed significant bathochromic shifts when protonated with trifluoroacetic acid in chloroform. The complexation of P3 with Fe3+ led to a significant absorption change and fluorescence quenching, and this implied the coordination of ferric ions with the 2,6‐pyridylene groups in the backbone. Moreover, both phenothiazylene‐containing P2 and P3 showed conspicuous PL quenching with a slight redshift when oxidized with NOBF4. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 1272–1284, 2004
Emulsion polymerization: From fundamental mechanisms to process developments
Authors: Asua José M.
Published: January 2004

Emulsion polymers are “products by process” whose main properties are determined during polymerization. In this scenario of margins reduction, increasing competition, and public sensitivity to environmental issues, the challenge is to achieve an efficient production of high‐quality materials in a consistent, safe, and environmentally friendly way. This highlight reviews the investigations carried out at The University of the Basque Country to develop a knowledge‐based strategy to achieve these goals. First, the research in fundamental mechanisms is discussed. This includes studies in radical entry and exit, oil‐soluble initiators, propagation‐rate constants of acrylic monomers, processes involved in the formation of branched and crosslinked polymers, microstructure modification by postreaction operations, the formation of particle morphology, and reactive surfactants. The advanced mathematical models developed in the group are also reviewed. In the second part, the advances in process development (optimization, online monitoring and control, monomer removal, production of high‐solids, low‐viscosity latices, and process intensification) are presented. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 1025–1041, 2004
From analysis of protein structural alignments toward a novel approach to align protein sequences
Authors: Sunyaev Shamil R. , Bogopolsky Gennady A. , Oleynikova Natalia V. , Vlasov Peter K. , Finkelstein Alexei V. , Roytberg Mikhail A.
Published: January 2004

Alignment of protein sequences is a key step in most computational methods for prediction of protein function and homology‐based modeling of three‐dimensional (3D)‐structure. We investigated correspondence between “gold standard” alignments of 3D protein structures and the sequence alignments produced by the Smith–Waterman algorithm, currently the most sensitive method for pair‐wise alignment of sequences. The results of this analysis enabled development of a novel method to align a pair of protein sequences. The comparison of the Smith–Waterman and structure alignments focused on their inner structure and especially on the continuous ungapped alignment segments, “islands” between gaps. Approximately one third of the islands in the gold standard alignments have negative or low positive score, and their recognition is below the sensitivity limit of the Smith–Waterman algorithm. From the alignment accuracy perspective, the time spent by the algorithm while working in these unalignable regions is unnecessary. We considered features of the standard similarity scoring function responsible for this phenomenon and suggested an alternative hierarchical algorithm, which explicitly addresses high scoring regions. This algorithm is considerably faster than the Smith–Waterman algorithm, whereas resulting alignments are in average of the same quality with respect to the gold standard. This finding shows that the decrease of alignment accuracy is not necessarily a price for the computational efficiency. Proteins 2003;9999:000–000. © 2003 Wiley‐Liss, Inc.
Substrate binding to mononuclear metallo‐β‐lactamase from Bacillus cereus
Authors: Dal Peraro Matteo , Vila Alejandro J. , Carloni Paolo
Published: January 2004

Structure and dynamics of substrate binding (cefotaxime) to the catalytic pocket of the mononuclear zinc‐β‐lactamase from Bacillus cereus are investigated by molecular dynamics simulations. The calculations, which are based on the hydrogen‐bond pattern recently proposed by Dal Peraro et al. (J Biol Inorg Chem 2002; 7:704–712), are carried out for both the free and the complexed enzyme. In the resting state, active site pattern and temperature B‐factors are in agreement with crystallographic data. In the complexed form, cefotaxime is accommodated into a stable orientation in the catalytic pocket within the nanosecond timescale, interacting with the enzyme zinc‐bound hydroxide and the surrounding loops. The β‐lactam ring remains stable and very close to the hydroxide nucleophile agent, giving a stable representation of the productive enzyme‐substrate complex. Proteins 2004;54:000–000. © 2003 Wiley‐Liss, Inc.
Comparison of the transition state ensembles for folding of Im7 and Im9 determined using all‐atom molecular dynamics simulations with ϕ value restraints
Authors: Paci Emanuele , Friel Claire T. , Lindorff‐Larsen Kresten , Radford Sheena E. , Karplus Martin , Vendruscolo Michele
Published: January 2004

Delineation of the structural properties of transition states is key to deriving models for protein folding. Here we describe the structures of the transition states of the bacterial immunity proteins Im7 and Im9 obtained by all‐atom molecular dynamics simulations with ϕ value restraints derived from protein engineering experiments. This pair of proteins is of special interest because, at pH 7 and 10 °C, Im7 folds via an intermediate while Im9 folds with a two‐state transition. The structures of the transition states for Im7 and Im9, together with their radii of gyration and distances from the native state, are similar. The typical distance between any two members of the transition state ensemble of both proteins is large, with that of Im9 nearly twice that of Im7. Thus, a broad range of structures make up the transition state ensembles of these proteins. The ensembles satisfy the set of rather low ϕ values and yet are consistent with high βT values (> 0.85 for both proteins). For both Im7 and Im9 the inter‐helical angles are highly variable in the transition state ensembles, although the native contacts between helices I and IV are well conserved. By measuring the distribution of the accessible surface area for each residue we show that the hydrophobic residues that are buried in the native state remain buried in the transition state, corresponding to a hydrophobic collapse to a relatively ordered globule. The data provide new insights into the structural properties of the transition states of these proteins at an atomic level of detail and show that molecular dynamics simulations with ϕ value restraints can significantly enhance the knowledge of the transition state ensembles (TSE) provided by the experimental ϕ values alone. Proteins 2004;54:000–000. © 2003 Wiley‐Liss, Inc.
Prediction of protein relative solvent accessibility with support vector machines and long‐range interaction 3D local descriptor
Authors: Kim Hyunsoo , Park Haesun
Published: January 2004

The prediction of protein relative solvent accessibility gives us helpful information for the prediction of tertiary structure of a protein. The SVMpsi method, which uses support vector machines (SVMs), and the position‐specific scoring matrix (PSSM) generated from PSI‐BLAST have been applied to achieve better prediction accuracy of the relative solvent accessibility. We have introduced a three‐dimensional local descriptor that contains information about the expected remote contacts by both the long‐range interaction matrix and neighbor sequences. Moreover, we applied feature weights to kernels in SVMs in order to consider the degree of significance that depends on the distance from the specific amino acid. Relative solvent accessibility based on a two state‐model, for 25%, 16%, 5%, and 0% accessibility are predicted at 78.7%, 80.7%, 82.4%, and 87.4% accuracy, respectively. Three‐state prediction results provide a 64.5% accuracy with 9%; 36% threshold. The support vector machine approach has successfully been applied for solvent accessibility prediction by considering long‐range interaction and handling unbalanced data. Proteins 2004;54:000–000. © 2003 Wiley‐Liss, Inc.
Structural principles of leucine‐rich repeat (LRR) proteins
Authors: Enkhbayar Purevjav , Kamiya Masakatsu , Osaki Mitsuru , Matsumoto Takeshi , Matsushima Norio
Published: January 2004

LRR‐containing proteins are present in over 2000 proteins from viruses to eukaryotes. Most LRRs are 20–30 amino acids long, and the repeat number ranges from 2 to 42. The known structures of 14 LRR proteins, each containing 4–17 repeats, have revealed that the LRR domains fold into a horseshoe (or arc) shape with a parallel β‐sheet on the concave face and with various secondary structures, including α‐helix, 310‐helix, and pII helix on the convex face. We developed simple methods to charactere quantitatively the arc shape of LRR and then applied them to all known LRR proteins. A quantity of 2Rsin(φ/2), in which R and φ are the radii of the LRR arc and the rotation angle about the central axis per repeating unit, respectively, is highly conserved in all the LRR proteins regardless of a large variety of repeat number and the radius of the LRR arc. The radii of the LRR arc with β‐α structural units are smaller than those with β‐310 or β‐pII units. The concave face of the LRR β‐sheet forms a surface analogous to a part of a Möbius strip. Proteins 2004;54:000–000. © 2003 Wiley‐Liss, Inc.
Is there a weak H‐bond → LBHB transition on tetrahedral complex formation in serine proteases?
Authors: Shokhen Michael , Albeck Amnon
Published: January 2004

The transformation of a weak hydrogen bond in the free enzyme into a low‐barrier hydrogen bond (LBHB) in the tetrahedral intermediate has been suggested as an important factor facilitating catalysis in serine proteases. In this work, we examine the structure of the H‐bond in the Asp102–His57 diad of serine proteases in the free enzyme and in a covalent tetrahedral complex (TC) with a trifluoromethylketone inhibitor. We apply ab initio quantum mechanical calculations to models consisting of a large molecular fragment of the enzyme active site, and the combined effect of the rest of the protein body and the solvation by surrounding bulk water was simulated by a self‐consistent reaction field method in our novel QM/SCRF(VS) approach. Potential profiles of adiabatic proton transfer in the Asp102–His57 diad in these model systems were calculated. We conclude that the hydrogen bond in both the free enzyme and in the enzyme‐inhibitor TC is a strong ionic asymmetric one‐well hydrogen bond, in contrast to a previous suggestion that it is a weak H‐bond in the former and a double‐well LBHB in the latter. Proteins 2004;54:000–000. © 2003 Wiley‐Liss, Inc.
Inhomogeneous stability of bacteriorhodopsin in purple membrane against photobleaching at high temperature
Authors: Yokoyama Yasunori , Sonoyama Masashi , Mitaku Shigeki
Published: January 2004

Heterogeneity 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

SCF 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

A 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

This 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

The 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

The 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

Depsipeptides, 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

Pigment‐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

A 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

A 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

This 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

SPARC 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

Solubility 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

This 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

A 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

A 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

The 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.
End‐to‐end QoS and global mobility management in an integrated satellite/terrestrial network
Authors: Conforto P. , Tocci C. , Schena V. , Secondiani L. , Blefari‐Melazzi N. , Chan P. M. L. , Delli Priscoli F.
Published: January 2004

For decades, the development of the Internet was driven by the purpose of providing applications to non‐mobile users. No specific Quality of Service (QoS) requirement is necessary, other than ensuring reliability in the end‐to‐end data transfers. As such, best effort service model was deemed more than appropriate to satisfy the users' needs. Nevertheless, the scenario has changed in the last few years. A new population of nomadic users, who requires access to Internet services regardless of their location and mode of transportation is growing, while new typologies of Internet applications are being continuously developed, in which best effort service level may no longer be adequate.

The SUITED project has been devised to address the emerging issues generated by this new and challenging scenario. SUITED aims at contributing towards the design and deployment of the Global Mobile Broadband System (GMBS), a unique satellite/terrestrial infrastructure, which will ensure that nomadic users have access to Internet services with a negotiated QoS. An overview of the main results achieved in the SUITED project is provided in this article. Some of the most innovative solutions developed by the SUITED team for the joint management of global mobility and end‐to‐end QoS support are presented. The SUITED demonstrator platform, which was developed to validate the system specifications, is also described. Finally, the results of the experimental measurement campaigns carried out with this platform are reported. Copyright © 2004 John Wiley & Sons, Ltd.
GAUSS satellite solution for location‐based services
Authors: Di Fazio Antonella , Mocci Gabriele , Rossini Eugenio , D'Angelo Giuseppe , Lorelli Andrea , Jarosh Andreas
Published: January 2004

The project was carried by an industrial Consortium, involving nine European companies, with proven experience and complementary skill in the fields of telecommunication, equipment manufacturing, communication and navigation system engineering, service provisioning. The GAUSS Team involves ARNI (Azienda Regionale per la Navigazione Interna, I), ASCOM (CH), ERICSSON Telecomunicazioni (I), GMV (E), TELEFONICA (E), THALES Navigation (F), TTI Norte (E), Space Engineering (I) and TELESPAZIO (I) as project co‐ordinator. The work allocation was in line with the companies market and technological prospects, in view of future developments taking benefits from the experience and know‐how acquired in the GAUSS project.

GAUSS objective was to design and demonstrate the feasibility of a system providing high quality Location‐based services, from the integration of Satellite Navigation and Communications, within the contexts of GALILEO and the UMTS technology.

The GAUSS solution addresses two classes of users profiles, belonging to info‐mobility and inter‐modality (road‐river) markets. It supports highly reliable, near real‐time two‐way communication between mobile users and service centre/provider.

GAUSS developed a system, which integrates advanced communication and precise navigation, for providing reliable and effective location‐based services oriented to transport and mobility applications (freight and fleet management, road safety and info‐mobility, emergency assistance, dangerous goods transportation control, inter‐modal transport). The GAUSS system combines off‐the‐shelf and new developed technologies, using S‐UMTS 3GPP compliant point‐to‐point and broadcasting packet‐based communication and GNSS1‐EGNOS accurate positioning. It has an open architecture ready to operate with the future GALILEO and UMTS, and further exploitation scenarios.

This paper provides an overview of the project and the main achieved results, along with their assessment and evaluation in terms of possible enhancements and future exploitations. Copyright © 2004 John Wiley & Sons, Ltd.
Advances of aeronautical communications in the EU framework
Authors: Holzbock Matthias , Hu Yim‐Fun , Jahn Axel , Werner Markus
Published: January 2004

This paper reports on the advancement in the research and development of aeronautical satellite communications within the EU framework. Starting from key aspects such as spectrum regulatory and marketing issues which affect the development of aeronautical communication systems, discussion on the motivation behind the two EU projects, ABATE and WirelessCabin and their interconnection then follows. ABATE concentrated on the development of an aeronautical communications system for flight routes in the European and Northern Atlantic regions. The enabling technology considered in ABATE is discussed. Major achievements and results obtained in the project are reported in this paper. These include the development of a powerful software tool based on a logical design methodology for aeronautical satellite communication systems as well as the characterization of the aeronautical channel through a series of channel measurement campaign and a demonstration of in‐flight multimedia satellite communication. The evolvement from ABATE to WirelessCabin is then highlighted. The main objective and current development of WirelessCabin since the start of the project are presented. In particular, issues on electromagnetic compatibility between different electronic equipments on board the aircraft cabin are discussed. Networking aspects for mobility, QoS and VPN support are studied. Specifically, different scenarios for the location management and address assignment schemes for mobility and VPN support are discussed in detail. Copyright © 2004 John Wiley & Sons, Ltd.
Multimedia services with QoS support in an integrated terrestrial and satellite UMTS network demonstrator: the IST VIRTUOUS project
Authors: Del Sorbo Filomena , Delli Priscoli Francesco
Published: January 2004

The integration of a terrestrial UMTS network with a satellite platform represents one of the most attractive proposals to develop a functional virtual home UMTS environment for a generic mobile user provided with an ‘ad hoc’ dual mode terminal, which will be able to exploit the two integrated systems (hereafter referred to as ‘segments’) for a set of innovative multimedia services. At this purpose, the IST research project ‘VIRTUOUS’ (virtual UMTS home on satellite) aimed at studying and implementing an integrated satellite and terrestrial UMTS (S‐UMTS, T‐UMTS) demonstrator in order to develop new multimedia services provided ‘anywhere for everyone’, targeting, at the same time, to an efficient exploitation of the satellite transmission capabilities. This paper deals with the description of the three major experiments were carried out on the VIRTUOUS demonstrator and with their achievements, i.e. (i) the development of a QoS supporting architecture (QoS experiment) for the T–S‐UMTS systems, (ii) the demonstration of advanced end‐user services (end user service experiment) and (iii) the achievement of a satisfactory user's mobility (inter segment roaming experiment).

The paper is organised as follows: first a general introduction of the VIRTUOUS project and of its demonstrator is given. Then the three above mentioned experiments are described in detail with particular emphasis to their results. Finally the paper is concluded by a brief summary of the main achieved results. Copyright © 2004 John Wiley & Sons, Ltd.