bluuebunny/crossref_metadata_2025_split huggingface dataset:
BKWC: An Empirical BKW Parametrization Based on Cylinder Test data
Authors: Fried Laurence E. , Clark Souers P. 
Published: May 2005

AbstractA database containing mostly cylinder test data for 42 explosives composed of C, N, O, H, F, and Cl was collected. The resulting detonation velocities, C‐J pressure, adiabat energies, and total energies of detonation were used to reparametrize the BKW equation of state for the CHEETAH thermochemical code. The resulting parameter set, referred to as BKWC, reproduces detonation velocities and adiabat energies better than previous BKW parametrizations. The BKWR equation of state is found to be slightly better in yielding C‐J pressures.
Synthetic peptides corresponding to sequences of snake venom neurotoxins and rabies virus glycoprotein bind to the nicotinic acetylcholine receptor
Authors: Lentz Thomas L. , Hawrot Edward , Wilson Paul T. 
Published: May 2005

AbstractPeptides corresponding to portions of loop 2 of snake venom curare‐mimetic neurotoxins and to a structually similar region of rabies virus glycoprotein were synthesized. Interaction of these peptides with purified Torpedo electric organ acetylcholine receptor was tested by measuring their ability to block the binding of 125I‐labeled α‐bungarotoxin to the receptor. In addition, inhibition of α‐bungarotoxin binding to a 32‐residue synthetic peptide corresponding to positions 173–204 of the α‐subunit was determined. Neurotoxin and glycoprotein peptides corresponding to toxin loop 2 inhibited labeled toxin binding to the receptor with IC50 values comparable to those of nicotine and the competitive antagonist d‐tubocurarine and to the α‐subunit peptides with apparent affinities between those of d‐tubocurarine and α‐cobratoxin. Substitution of neurotoxin residue Arg37, the proposed counterpart of the quatenary ammonium of acetylcholine, with a negatively charged Glu residue reduced the apparent affinity about 10‐fold. Peptides containg the neutotoxin invarint residue Trp29 had 10‐ to 100‐fold higher affinites than peptides lacking this residue. These results demonstrate that relatively short synthetic peptides retain some of binding ability of the native protein from which they are derived, indicating that such peptides are useful in the study of proetin interactions. The ability of the peptides to compete α‐bungarotoxin binding to the receptor with apparent affinites comparable to those of other cholinergic ligands indicates that loop 2 of the neurotoxins and the strucually similar segment of the rabies virus glycoprotein act as recognition sites for the acetylcholine receptor. Invarient toxin residues Arg37 and Trp29 and their viral homologs play important, although not essential, roles in binding, possibly by interaction with complementary anionic and hydrophobic subsites on the acetylcholine receptor. The α‐subunit peptide most likely contains all of the determinants for binding of the toxin and glycoprotein peptides present on the α‐subunit, because these peptides bind to the 32‐residue α‐subunit peptides with the same or greater affinity as to the intact subunit.
Calibration of effective van der Waals atomic contact radii for proteins and peptides
Authors: Iijima Hiroshi , Dunbar James B. , Marshall Garland R. 
Published: May 2005

AbstractEffective van der Waals radii were celebrated in such a way that molecular models built from standard bond lengths and bond angels reproduced the amino acid conformations observed by crystallography in proteins and peptides. The celebrations were based on the comparision of the Ramachandbran plots prepared from high‐resolution X‐ray data of protins and peptides with the allowed ϕ,ψ torsional angel space for the depeptide molecular models. The celebrated radii are useful as criteria with which to filter energetically improbable conformations in molecular modeling studies of proteins and peptides.
Crystal structure of subtilisin BPN′ variants containing disulfide bonds and cavities: Concerted structural rearrangements induced by mutagenesis
Authors: Katz Bradley , Kossiakoff Anthony A. 
Published: May 2005

AbstractThe X‐ray structure of four genetically engineered disulfide variants of subtilisin have been analyzed to determine the energetic and structural constraints involved in inserting disulfide bonds into proteins. Each of the engineered disulfides exhibited atypical sets of dihedral angles compared with known structures of natural disulfide bridges in proteins and affected its local structural environment to a different extent. The disulfides located in buried regions, Cys26–Cys232 and Cys29–Cys87 and Cys22–Cys87, which are located on the surface of the molecule. An analysis of the concerted changes in secondary structure units such as α‐helices and β‐sheets indicated systematic long‐range effects. The observed changes in the mutants were largely distributed asymmetrically around the inserted disulfides, reflecting different degrees of inherent flexibility of neighboring secondary structure types. The disulfide substitution in each variant molecule created some invaginations or cavities, causing a reorganization of the surrounding water structure. These changes are described, as well as the changes in side chain positions of groups that border the cavities.
Analysis of solvent structure in proteins using neutron D2OH2O solvent maps: Pattern of primary and secondary hydration of trypsin
Authors: Kossiakoff Anthony A. , Sintchak Michael D. , Shpungin Joseph , Presta Leonard G. 
Published: May 2005

AbstractA method of determining the water structure in protein crystals is described using neutron solvent difference maps. These maps are obtained by comparing the changes in diffracted intensities between two data sets, one in which H2O is the major solvent constituent, and a second in which D2O is the solvent medium. To a good first approximation, the protein atom contributions to the scattering intensities in both data sets are equal and cancel, but since H2O and D2O have very different neutron‐scattering properties, their differences are accentuated to reveal an accurate representation of the solvent structure. The method also employs a series of density modification steps that impose known physical constraints on the density distribution function in the unit cell by making real space modifications directly to the density maps. Important attributes of the method are that (1) it is less subjective in the assignment of water positions than X‐ray analysis; (2) there is threefold improvement in the signal‐to‐noise ratio for the solvent density; and (3) the iterative density modification produces a low‐biased representation of the solvent density. Tests showed that water molecules with as low as 10% occupancy could be confidently assigned.About 300 water sites were assigned for trypsin from the refined solvent density; 140 of these sites were defined in the maps as discrete peaks, while the remaining were found within less‐ordered channels of density. There is a very good correspondence between the sites in the primary hydration layer and waters found in the X‐ray structure. Most water sites are clustered into H‐bonding networks, many of which are found along intermolecular contact zones. The bound water is equally distributed between contacting apolar and polar atoms at the protein interface. A common occurence at hydrophobic surfaces is that apolar atoms are circumvented by one or more waters that are part of a larger water network. When the effects on surface accessibility by neighboring molecules in the crystal lattice are taken into consideration, only about 29% of the surface does not interface ordered water. About 25% of the ordered water is found in the second hydration sphere. In many instances these waters bridge larger clusters of primary layer waters. It is apparent that, in certain regions of the crystal, the organization of ordered water reflects the characteristics of the crystal environment more than those of trypsin's surface alone.
A novel approach to predicting protein structural classes in a (20–1)‐D amino acid composition space
Authors: Chou Kuo‐Chen 
Published: May 2005

AbstractThe development of prediction methods based on statistical theory generally consists of two parts: one is focused on the exploration of new algorithms, and the other on the improvement of a training database. The current study is devoted to improving the prediction of protein structural classes from both of the two aspects. To explore a new algorithm, a method has been developed that makes allowance for taking into account the coupling effect among different amino acid components of a protein by a covariance matrix. To improve the training database, the selection of proteins is carried out so that they have (1) as many non‐homologous structures as possible, and (2) a good quality of structure. Thus, 129 representative proteins are selected. They are classified into 30 α, 30 β, 30 α + β, 30 α/β, and 9 ζ (irregular) proteins according to a new criterion that better reflects the feature of the structural classes concerned. The average accuracy of prediction by the current method for the 4 × 30 regular proteins is 99.2%, and that for 64 independent testing proteins not included in the training database is 95.3%. To further validate its efficiency, a jackknife analysis has been performed for the current method as well as the previous ones, and the results are also much in favor of the current method. To complete the mathematical basis, a theorem is presented and proved in Appendix A that is instructive for understanding the novel method at a deeper level. © 1995 Wiley‐Liss, Inc.
Crystallization and preliminary X‐ray investigation of the recombinant Trypanosoma brucei rhodesiense calmodulin
Authors: El‐Sayed Najib M. A. , Patton Curtis L. , Harkins Paul C. , Fox Robert O. , Anderson Karen 
Published: May 2005

AbstractBipyramidal crystals of the recombinant calmodulin from Trypanosoma brucei rhodesiense were obtained by vapor diffusion against 55% (v/v) 2‐methyl‐2,4‐pentanediol in 0.05 M cacodylate buffer, pH 5.6. When few nucleation events occurred, crystals grew to 0.25 × 0.25 × 1.20 mm. The space group of the crystal is I4122, with unit cell dimensions a = b = 56.88 Å, c = 230.11 Å, α = β = γ = 90°, z = 16. The molecular mass and volume of the unit cell suggest that there is one molecule in the asymmetric unit. The I/σ(I) ratio for data at 3.0 Å resolution was 3.67, indicating that the final structure can be refined at higher resolution. Molecular replacement methods and the PC‐refinement technique have not yet yielded the structure under a variety of search conditions. We are currently investigating the multiple isomorphous replacement approach to determine this crystal structure. © 1995 Wiley‐Liss, Inc.
Electron avalanche desorption: A new soft‐ionization technique for non‐volatile and/or thermally labile molecules
Authors: Zubarev R. A. , Bondarenko P. V. , Knysh A. N. , Rozynov B. V. 
Published: May 2005

AbstractA new ionization technique based on a modification of the conventional plasma‐desorption mass spectrometric apparatus is described. An electron avalanche produced by the microchannel plates of a secondary electron multiplier is found to desorb a sufficient amount of (quasi‐)molecular ions of non‐volatile thermally labile molecules. Spectra of several substances with molecular masses up to 1250 u are presented. The mechanism of electron avalanche desorption is now under investigation.
Structural dependence of anion/dipole complex upon the deprotonated site in [MH]− ions of 17β‐estradiol‐17‐stearate ester in ammonia negative‐ion chemical ionization
Authors: Fournier F. , Tabet J. C. , Debrauwer L. , Rao D. , Paris A. , Bories G. 
Published: May 2005

AbstractUnder ammonia negative‐ion chemical ionization (NICI), of 17β‐estradiol‐17‐stearate ester, a deprotonation reaction occurs competitively at two acidic positions(i.e., the phenol and enolizable sites), demonstrated by using gas phase labelling NICI conditions which yield both [MdD]− and [MdH]− ions. Investigation under low‐energy collisionally‐activated dissociation (CAD) of both molecular species indicates that prior to dissociation, each molecular species isomerizes into different ion/dipole intermediates. These complexes can lead to labile proton exchange. Dissociation of these complexes gives rise to the formation of complementary daughter ions whose abundance depends upon the relative gas phase acidity of the corresponding neutrals.
Mass spectrometry of laser‐desorbed oligonucleotides
Authors: Tang K. , Allman S. L. , Chen C. H. 
Published: May 2005

AbstractVarious matrices were used for laser‐desorption ionization of mixtures of small DNA segments. Parent negative ions of 34‐mer as well as other smaller single‐stranded oligomers were observed for selected organic acids and dye compounds. Both positive and negative parent ions were observed with very little fragmentation. Effects of various matrices and the potential applications to DNA sequencing are briefly discussed.
Matrix‐assisted laser desorption/ionization mass spectrometry of synthetic oligodeoxyribonucleotides
Authors: Parr Gary R. , Fitzgerald Michael C. , Smith Lloyd M. 
Published: May 2005

AbstractMatrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry has been used to mass analyze a variety of synthetic oligodeoxyribonucleotides ranging in size from 6 to 30 nucleotides. Molecular ions were observed almost exclusively, with little or no fragmentation and generally minor contributions from multiply charged species. Mixtures of poly d(T)12–30 with low picomole amounts of each component gave well resolved peaks. These results are encouraging for the concept of DNA sequence analysis by mass spectrometry.
Electrospray ionization tandem mass spectrometry of mixtures: Deconvolution by parent‐ion scans
Authors: Smith Philip B. , Snyder A. Peter 
Published: May 2005

AbstractElectrospray ionization (ESI) mass spectra equine myoglobin and a mixture of bovine insulin, melittin and bovine growth hormone releasing factor (GHRF) were obtained on a tandem quadrupole mass spectrometer. The parent‐ion mass spectrum of m/z 171 for equine myoglobin contained all of the multiply charged molecular ions present in the conventional ESI mass spectrum. Similar results were obtained with the parent‐ion scans of selected ions for the insulin, melittin and GHRF mixture. This technique was able to differentiate between the multiply charged molecular ions produced from each of the three componenets in the mixture.
New gas‐chromatographic/mass spectrometric method for the quantitative analysis of primary aromatic amines in main‐ and side‐stream cigarette smoke. I
Authors: Pieraccini G. , Luceri F. , Moneti G. 
Published: May 2005

AbstractA sensitive and accurate method to quantitate 17 primary aromatic amines in tobacco smoke has been set up. two Italian commercial brands of cigarette were smoked in a home‐made smoking machine; the amines in the smoke were trapped in dilute hudrochloric acid (containing 2H5‐aniline, 13C1‐o‐toluidine and 2H9‐4‐aminobiphenyl as internal standards) and, after extraction and purification, derivatized as pentafluoropro‐pionamides and measured by gas chromatography/mass spectrometry in the selected‐ion‐monitoring mode. Our results confirmed that side‐stream smoke contains total levels of aromatic amines about 50–60 times higher than those of main‐stream smoke of black‐tobacco cigarettes is richer in aromatic amines compared to light‐tobacco cigarettes.
Detection of γ‐aminobutyric acid in a rat brain using in vivo microdialysis‐capillary electrophoresis/mass spectrometry
Authors: Takada Yasuaki , Yoshida Motoko , Sakairi Minoru , Koizumi Hideaki 
Published: May 2005

AbstractCoupling of in vivo microdialysis with capillary electrophoresis/mass spectrometry (MD‐CE/MS) was demonstrated. A microdialysis probe was inserted in the striatum of a rat brain and γ‐aminobutyric acid (GABA) in the brain was detected by CE/MS without any chemical treatment of the sample. MD‐CE/MS is expected to be a useful technique for analyzing brain substances, because of the relatively small damage it causes to a living structure and the high selectivity of the analytical technique.
Urinary porphyrin profiles by laser desorption/ionization time‐of‐flight mass spectrometry without the use of classical matrices
Authors: Jones Russell M. , Lamb John H. , Lim Chang Kee 
Published: May 2005

AbstractA method is described for the rapid analysis of mixtures of porphyrin methyl esters using laser desorption/ionization time‐of‐flight mass spectrometry (LDI‐TOF MS). Ions corresponding to [M+H]+ for each component have been observed without the need for added matrix. LDI‐TOF MS has been applied to the analysis and characterization of porphyrin methyl esters derived from urine samples of patients suffering from various porphyrias. This technique has been shown to provide ‘fingerprint’ profiles of the porphyrins present in each urine sample, characteristic of the porphyria, which compare favourably with those obtained with the established method of high‐performance liquid chromatography. LDI‐TOF MS is a rapid and reliable method for the screening of urine from patients suffering from porphyria.
Analysis of polychlorinated biphenyls by quadrupole ion trap mass spectrometry. Part II: Comparison of mass spectrometric detection using electron impact and selected‐ion chemical ionization with electron capture detection
Authors: Lausević M. , Jiang X. , March R. E. , Metcalfc C. D. 
Published: May 2005

AbstractThe responses of selected‐ion monitoring of electron impact mass spectra and selected‐reagent‐ion chemical ionization mass spectra of polychlorinated biphenyls (PCBs), relative to that of congener 153, have been determined for some 60 PCBs contained in four standard mixtures. The PCB congeners examined cover a wide range of toxicities. Average responses have been determined for PCBs as a function of both the total number of chlorine substituents and the number of ortho‐substituents. Average relative responses and relative responses of individual congeners have been compared with Literature values of relative responses obtained by electron‐capture detection. Detection limits for electron ionization and C2H chemical ionization mass spectrometry, determined as the mass of congener 153 injected on column and yielding a signal‐to‐noise ratio of 5:1 were 0.76 pg and 30 pg, respectively, compared to some 70 fg for electron‐capture detection. An initial exploration and evaluation have been carried out, of the potential value of using a toxicity index to define the total toxicity of a sample; such an index is based on 39 non‐ and mono‐ortho substituted PCBs. Electron ionization, when combined with selected‐ion monitoring of both molecular and fragment ions, is the more sensitive mass‐selective method for the determination of the most toxic PCB congeners.
Matrix‐assisted laser desorption/ionization mass spectrometry of polysaccharides
Authors: Garrozzo Domenico , Impallomeni Giuseppe , Spina Emanuela , Sturiale Luisa , Zanetti Flavio 
Published: May 2005

AbstractIn this paper we report matrix‐assisted laser desorption/ionization (MALDI) mass spectra of dextrans up to 100 000 Da molecular weight and compare these measurements with those obtained by conventional size‐exclusion chromatography with low‐angle laser light scattering (SEC/LALLS). These results extend the usefulness of MALDI‐MS to higher molecular weight polysaccharides and give some insights into the MALDI process.
Mass spectrometric investigations of some N‐cycloalkyl and N‐aryl fluoroacetamides
Authors: Jeremić Ljiljana A. , Perić Aleksandra A. , Stojanović Nadežda D. , Petrović Slobodan D. 
Published: May 2005

AbstractThe electron‐ionization induced mass spectra of some N‐monosubstituted fluoroacetamides of the general formula FCH2CONHR, in which the substituent R is (C3C7) cycloalkyl, phenyl, 4‐methylphenyl, 4‐carbo‐methoxyphenyl, 4‐nitrophenyl and 4‐diethylaminophenyl, were recorded and their fragmentation patterns were studied by metastable‐ion analyses.
A simple method for removing overlapped Auger signals from ELS or low energy reflection mode EXELFS
Authors: Matsuta Hideyuki , Hirokawa Kichinosuke 
Published: May 2005

AbstractTwo simple techniques are described for eliminating overlapped intense Auger signals from electron energy loss spectrum. One is performed by superimposing a small oscillation on both the sample and the CMA band pass energy and detecting only signals which are not altered by the modulation, the other is performed by applying large bias voltage to the sample. These techniques can be used to extract the low energy reflection mode extended electron energy loss fine structure (EXELFS) signals.
Interfacial chemistry at real resin–metal interfaces of electronics devices
Authors: Pignataro S. , Torrisi A. , Ferla G. 
Published: May 2005

AbstractAn amine and an anhydride cured commercial epoxy resin were moulded to real Ag, Ni and Cu surfaces in plant conditions. The joints were mechanically broken and the two faces obtained in the fracture analysed by ESCA. The interfacial chemical compositions were found to be different with respect to that of the corresponding resin and metal bulk.Some of the resin constituents were confined in the bulk of the resin itself. Others were found to be homogeneously distributed between the bulk of the resin and the interface. Another group of resin constituents were found to segregate to the interfacial zone, often in a chemical state different from that found in the bulk. Also some trace elements present as additives in the metals were found to migrate to the interfacial zone.The migration phenomena were found to selectively depend on the chemical nature of the metal and resin respectively. Dramatic chemical composition differences were found between the two faces obtained in the fracture.The effect of time and moulding temperature on the interfacial chemistry was studied. Proof of various chemical reactions taking place at the interfaces with time or moulding temperature could be obtained.The results are discussed also in terms of performance of the electronic devices where the studied interfaces are present.
Glow discharge sputtering of alloys observed by atomic absorption spectroscopy
Authors: Teo W. B. , Hirokawa K. 
Published: May 2005

AbstractSputtering procedures are often employed in the field of material preparation such as thin films and surface analysis. In this report the atomic absorption spectroscopic technique is applied to observe sputtering phenomena of typical binary alloys of copper–nickel and coppersilver, as occurring in a hollow cathode glow discharge. A parameter μα−β correlating the composition of the sample with the composition of the produced plasma which was measured with atomic absorption spectroscopy, is used to monitor changes in the surface composition. Measurements at a natural high surface temperature of the sample during glow discharge and at a lower temperature by cooling with liquid nitrogen were performed. AES analysis of the glow discharge sputtered surfaces of uncooled samples show that a very deep altered layer can be produced.
An AES and ELS study of InP (100) surface subjected to argon ion bombardment
Authors: Jardin C. , Robert D. , Achard B. , Gruzza B. , Pariset C. 
Published: May 2005

AbstractAuger electron spectroscopy (AES) and electron loss spectroscopy (ELS) have been performed in order to investigate a (100) InP surface subjected to argon ion bombardment at low energy. It has been found that preferential sputtering of phosphorus‐impurities species during the cleaning stage results in the formation of a In0.57P0.43 disordered layer. Within the sampling depth of the In MNN Auger electrons, about 1/4 of the total In atoms are of metallic type. Our experimental results are not consistent with the formation of pure In islands over a stoichiometric InP surface. If In clusters are present in the disordered surface, they are associated with adsorbed phosphorus. Prolonged ion bombardment increases the surface roughness as detected by ELS and scanning electron microscopy (SEM).