bluuebunny/crossref_metadata_2025_split huggingface dataset:
Crystallization and X‐ray diffraction data of the cleaved form of plasminogen activator inhibitor‐1
Authors: Aertgeerts K. , De Bondt H. L. , De Ranter C. , Declerck P. J. 
Published: May 2005

AbstractTo characterize the structural requirements for the conformational flexibility in plasminogen activator inhibitor‐1 (Pal‐1) we have crystallized human PAI‐1, carrying a mutation which stabilizes PAI‐1 in its substrate form. Crystallization was performed by the hanging drop diffusion method at pH 8.5 in the presence of 19% (w/v) polyethyleneglycol 4000 as a precipitant. The crystals appear after 3 days at 23°C and belong to the monoclinic space group C2 with cell dimensions of a=151.8 Å, b=47.5 Å, c=62.7 Å, and β=113.9°, and one molecule in the asymmetric unit. The X‐ray diffraction data set contains data with a limiting resolution of 2.5 Å. Biochemical analysis of the redissolved crystals indicated that during the crystallization process, cleavage had occurred in the active site loop at the P1‐P1′ position. The availability of good‐quality crystals of the cleaved form of this serpin will allow its three‐dimensional structure to be solved and will provide detailed information on the structure‐function relationship in PAI‐1. © 1995 Wiley‐Liss, Inc.
Crystallization of a soluble, catalytically active form of Escherichia coli leader peptidase
Authors: Paetzel Mark , Chernaia Maia , Strynadka Natalie , Tschantz William , Cao Gnoqing , Dalbey Ross E. , James Michael N. G. 
Published: May 2005

AbstractLeader peptidase, a novel serine protease in Escherichia coli, catalyzes the cleavage of the amino‐terminal leader sequences from exported proteins. It is an integral membrane protein containing two transmembrane segments with its carboxy‐terminal catalytic domain residing in the periplasmic space. Here, we report a procedure for the purification and the crystallization of a soluble non‐membrane‐bound form of leader peptidase (Δ2‐75). Crystals were obtained by the sitting‐drop vapor diffusion technique using ammonium dihydrogen phosphate as the precipitant. Interestingly, we have found that the presence of the detergent Triton X‐100 is required to obtain crystals sufficiently large for X‐ray analysis. The crystals belong to the tetragonal space group P42212, with unit cell dimensions of a = b = 115 Å and c = 100 Å, and contain 2 molecules per asymmetric unit. This is the first report of the crystallization of a leader (or signal) peptidase. © 1995 Wiley‐Liss, Inc.
Crystallization and preliminary crystallographic analysis of recombinant abrin‐a A‐chain with ribosome inactivating Activity
Authors: Kohno Tetsuya , Senda Toshiya , Narumi Hideki , Kimura Shigenobu , Mitsui Yukio 
Published: May 2005

AbstractCrystals have been obtained for a recombinant abrin‐a A‐chain produced by E. coli. The crystals were grown using PEG6000 as the precipitating agent. The crystals belong to an orthrhombic space group P 212121 and diffract to 1.7 Å. © 1995 Wiley‐Liss, Inc.
Perfect temperature for protein structure prediction and folding
Authors: Finkelstein Alexei V. , Gutin Alexander M. , Badretdinov Azat Ya. 
Published: May 2005

AbstractWe have investigated the influence of the “noise” of inevitable errors in energetic parameters on‐protein structure prediction. Because of this noise, only a part of all the interactions operating in a protein chain can be taken into account, and therefore a search for the energy minimum becomes inadequate for protein structure prediction. One can rather rely on statistical mechanics: a calculation carried out at a temperature T* somewhat below that of protein melting gives the best possible, though always approximate prediction. The early stages of protein folding also “take into account” only a part of all the interactions; consequently, the same temperature T* is favorable for the self‐organization of native‐like intermediates in protein folding. © 1995 Wiley‐Liss, Inc.
Kinetic folding and unfolding of staphylococcal nuclease and its six mutants studied by stopped‐flow circular dichroism
Authors: Kalnin Nikolay N. , Kuwajima Kunihiro 
Published: May 2005

AbstractKinetics of refolding and unfolding of staphylococcal nuclease and its six mutants, each carrying single or double amino acid substitutions, are studied by stopped‐flow circular dichroism measurements. A transient kinetic intermediate formed within 10 ms after refolding starts possesses a substantial part of the N‐domain core β‐structure, whereas helices are formed at the later stages. The structure of the kinetic intermediate is less organized than the structure that is known to be formed by a nuclease 1‐136 fragment. Only the refolding kinetics are affected by the mutations in all the mutants except two in which the mutations have changed the native structure. From this result and also from the locations of the mutation sites, the major N‐terminal domain of the nuclease in the transition state of folding has a structure nearly identical to the native one. On the other hand, the minor C‐terminal domain has previously been shown to be still disorganized in the transition state. The effects of the amino acid substitutions on the stability of the native and the transition states are in good agreement with the changes in the hydration free energy, expected for the corresponding amino acid replacements in the unfolded polypeptide. Since side chains of all the mutated residues are not accessible to solvent in the native structure, the result suggests that it is the unfolded state that is mainly affected by the mutations. © 1995 Wiley‐Liss, Inc.
Purification, characterization, crystallization, and preliminary X‐ray results from Paracoccus denitrificans porin
Authors: Hirsch Andreas , Wacker Thomas , Weckesser Jürgen , Diederichs Kay , Welte Wolfram 
Published: May 2005

AbstractThe porin from Paracoccus denitrificans ATCC 13543 was purified and crystallized. Two crystal forms were obtained from porin solutions with β‐d‐octylglucopyra‐noside as detergent. Crystals of form I belong to the monoclinic spacegroup C2 with unit cell dimensions a = 112.2 Å, b = 193.8 Å, c = 100.5 Å and β = 129.2°. There is 1 trimer per asymmetric unit. Crystals of form II are triclinic with α = 89.7 Å, b = 98.8 Å, c = 112.5 Å, b = 112.5Å, β = 101.8°, γ = 106.7° (2 trimers per asymmetric unit). Both crystal forms diffract to 3 Å. © 1995 Wiley‐Liss, Inc.
Crystallization of a membrane pore‐forming protein with mosquitocidal activity from Bacillus thuringiensis subspecies kyushuensis
Authors: Li Jade , Koni Pandelakis A. , Ellar David J. 
Published: May 2005

AbstractCytB, a membrane pore‐forming toxin from Bacillus thuringiensis subspecies kyushuensis, is specifically toxic to dipteran insect larvae but broadly cytolytic in vitro. It has been purified in the protoxin form from a recombinant Escherichia coli source and crystals have been obtained which diffract X‐rays to at least 2.6 Å resolution. The tendency for CytB to aggregate in solution was overcome by including 50 mM of urea or 8 mM of ethanolamine during crystallization. Mutants designed to add or subtract single cysteine residues for the purpose of heavy atom derivative preparation were similarly purified and crystallized. The crystals are hexagonal bipyramids. They belong to space group P6122 (or P6522) with lattice constants a = b = 67.34 Å, c = 170.96 Å, and contain one molecule of the CytB protoxin (MW 29235) per asymmetric unit and 27% solvent by volume. © 1995 Wiley‐Liss, Inc.
Assessment of a protein fold recognition method that takes into account four physicochemical properties: Side‐chain packing, solvation, hydrogen‐bonding, and local conformation
Authors: Matsuo Yo , Nishikawa Ken 
Published: May 2005

AbstractA protein fold recognition method was tested by the blind prediction of the structures of a set of proteins. The method evaluates the compatibility of an amino acid sequence with a three‐dimensional structure using the four evaluation functions: side‐chain packing, solvation, hydrogen‐bonding, and local conformation functions. The structures of 14 proteins containing 19 sequences were predicted. The predictions were compared with the experimental structures. The experimental results showed that 9 of the 19 target sequences have known folds or portions of known folds. Among them, the folds of Klebsiella aerogenes urease β subunit (KAUB) and pyruvate phosphate dikinase domain 4 (PPDK4) were successfully recognized; our method predicted that KAUB and PPDK4 would adopt the folds of macromomycin (Ig‐fold) and phosphoribosylanthra‐nilate isomerase:indoleglycerol‐phosphate synthase (TIM barrel), respectively, and the experimental structure revealed that they actually adopt the predicted folds. The predictions for the other targets were not successful, but they often gave secondary structural patterns similar to those of the experimental structures. © 1995 Wiley‐Liss, Inc.
Fold recognition and ab initio structure predictions using hidden markov models and β‐strand pair potentials
Authors: Hubbard Tim J. , Park J. 
Published: May 2005

AbstractProtein structure predictions were submitted for 9 of the target sequences in the competition that ran during 1994. Targets sequences were selected that had no known homology with any sequence of known structure and were members of a reasonably sized family of related but divergent sequences. The objective was either to recognize a compatible fold for the target sequence in the database of known structures or to predict ab initio its rough 3D topology. The main tools used were Hidden Markov models (HMM) for fold recognition, a β‐ strand pair potential to predict β‐sheet topology, and the PHD server for secondary structure prediction. Compatible folds were correctly identified in a number of cases and the β‐strand pair potential was shown to be a useful tool for ab initio topology prediction. © 1995 Wiley‐Liss, Inc.
Crystallization of the complex of human IFN‐γ and the extracellular domain of the IFN‐γ receptor
Authors: Chiène Christiane , Fountoulakis Michael , Döbeli Heinz , D'Arcy Brigitte , Winkler Fritz , D'Arcy Allan 
Published: May 2005

AbstractA complex of human interferon‐γ (IFN‐ γ) with the soluble extracellular domain of the IFN‐ γ receptor α‐chain (IFN‐γ‐R) has been crystallised. Crystals of the complex were grown using PEG 4000 as the precipitating agent in the presence of β‐octyl glucoside. The receptor‐ligand complex crystallizes in a monoclinic space group and diffracts to about 3.0 Å resolution. Isomorphous crystals have been obtained with complex containing selenomethionine and cysteine mutants of IFN‐γ, which may facilitate the ongoing X‐ray structure determination. © 1995 Wiley‐Liss, Inc.
Reaction‐induced mass discrimination in XQQ instruments. Absolute cross‐sections for N + SF6 → N2 + SF (x=1–5)
Authors: Martinez Richard I. , Ganguli B. , Boyd R. K. 
Published: May 2005

AbstractDynamically‐correct branching ratios can be measured in a XQQ tandem mass spectrometer (MS/MS) under single‐collision conditions when the key MS/MS parameters are properly selected to correct for reaction‐induced mass discrimination within the RF‐only quadrupole mass filter (Q2). The energy dependence of the cross‐section, σ(E), for the reaction N + SF6 → N2+SFx+ (x = 1–5) was measured in the NBS triple quadrupole (QQQ) tandem mass spectrometer. For P≃0.02–0.13 mTorr and E ≃ 5–60 eV (Lab) [the range of collision energies used for collisionally activated dissociation (CAD)], identical σ(E) were measured from both the rate of reactant ion decay and the rate of product ion formation. Therefore, these σ values are substantially free from kinetic interferences (i.e., no back reactions, no impurity reactions, no scattering losses, minimal fringing fields, no mass discrimination, well‐defined gas target, etc.). Moreover, there is probably no significant systematic error in our measurements of the absolute σ values for N + SF6 → N2+SF (x = 1–5) because the σ values we measured with this same technique for Ne +˙+ Ne → Ne+Ne+˙, Ar+˙ + Ar → Ar+Ar+˙, and Ar+˙+N2 → Ar+N agreed well with literature values obtained with several well‐established techniques.
Obtaining structural information of perfluoro‐1,3‐dimethyladamantane from collisionally activated decomposition mass spectra
Authors: Huang Sunkwei , Klein David H. , Adcock James L. , Gross Michael L. 
Published: May 2005

AbstractCyclic, high molecular weight perfluorocarbons (PFC's) are very electronegative, and can be detected by methane negative ion chemical ionization (NICI); however only molecular ions are detected. Electron ionization (EI) of PFC's, on the other hand, yields little or no molecular ion but very intense low mass fragment ions such as CF (m/z 69), C3F (m/z 131) and C4F (m/z 181), which are not structurally characteristic. High‐energy collisionally activated decomposition (CAD) of positive, molecular ions of perfluoro‐1,3‐dimethyladamantane yields important structural information by providing more intense high mass fragment ions. Fragments of the following formulae and abundances (in brackets): C5F (100), C11F (73), C7F (67), C8F (43), C4F (26), C7F (18), and CF (14) are detected by this method.
An experimental investigation of the possibility of developing a database for tandem mass spectrometry using xqq instruments
Authors: Dheandhanoo Seksan , Boyd R. K. 
Published: May 2005

AbstractThe NBS round‐robin protocol for testing the performance of XQQ tandem mass spectrometers (R.I. Martinez, Rapid Commun. Mass. Spectrom. 2, 8 (1988)) has been evaluated using a QQQ instrument which is significantly different in both the size of the quadrupole rods and the design from that used in the NBS work. The NBS experimental cross‐sections for the Ar+./Ar charge‐transfer reactions were used to provide a calibration of target thickness in the present apparatus. The present experimental value of the reaction cross‐section for the N2+./SF6 system is 60 ± 3 Å2 at the center‐of‐mass collision energy of 4.4 eV, in excellent agreement with the NBS literature value (55 Å2). This result supports the view that a library of collisionally activated dissociation spectra is feasible provided that the instruments used are of dynamically correct design.
Negative ion mass spectrometry of silylated cytokinins
Authors: Hocart Charles H. , Schlunegger Urs P. 
Published: May 2005

AbstractThe negative ion mass spectra or trimethylsilylzeatin riboside and t‐butyldimethylsilylzeatin, generated using either ammonia or 10% CO2/Ar as reagent gas, are described. Optimal yields of [M‐H]− ions were obtained with a source pressure of 5 Pa in the electron ionization source of a ZAB‐2F mass spectrometer, compared with 15 Pa to generate [M+H]+ in the chemical ionization mode. At 15 Pa no negative ions could be observed.
Fast‐atom bombardment tandem mass spectrometry of phosphohydroxylysine and related phosphohydroxy amino acids
Authors: Kulik W. , Heerma W. , Dorland L. , de Bree P. K. , Duran M. 
Published: May 2005

AbstractPhosphohydroxylysine a compound found in the urine of two patients with a possible inborn error of hydroxylysine metabolism, and related phosphohydroxycompounds were investigated with fast‐atom bombardment tandem mass spectrometry techniques. This resulted in a reliable and quick identification method for phospho amino acids in general.
Isomerization of proton‐bound alcohol dimers
Authors: Audier H. E. , Monteiro C. , Mourgues P. , Robin D. 
Published: May 2005

AbstractProton‐bound dimers [ROH… \documentclass{article}\pagestyle{empty}\begin{document}$ \mathop {\rm H}\limits^ + $\end{document}… HOR] have been studied under chemical ionization conditions. The structures of the fragment ions and the behaviour of variously deuterated ions when R = iC3H7 lead to a proposed fragmentation pathway.
Characterization of high molecular weight macrocycles by desorption chemical ionization mass spectrometry
Authors: Guglielmetti Gianfranco , Dalcanale Enrico , Bonsignore Stefanio , Vincenti Marco , Busch K. L. 
Published: May 2005

AbstractA series of multi‐armed macrocycles with molecular weights up to 4400 Da was studied by desorption chemical ionization. Both negative‐ and positive‐ion spectra exhibited excellent signal‐to‐noise ratio, despite the limited amount of material sampled (0.1–1 pmol). The molecular ions generally represent the base peaks of the spectra, but the extent of fragmentation increases as the source temperature is raised.
Direct analysis of drugs by continuous‐flow fast‐atom bombardment and tandem mass spectrometry
Authors: Seifert William E. , Ballatore Annie , Caprioli Richard M. , Boyd R. K. 
Published: May 2005

AbstractThe techniques of continuous‐flow fast‐atom bombardment (CF‐FAB) and tandem mass spectrometry (MS/MS) are combined and applied to the analysis of small molecular mass drugs (mol.wt < 500 Da). The approach involves the interfacing of a CF‐FAB inlet with a triple‐stage quadrupole mass spectrometer, enabling the acquisition of collision‐activated decomposition mass spectra of the drugs after FAB ionization. The relationship between a stable sample surface on the CF‐FAB probe tip and the quality of the mass spectrum is discussed, as are practical methods for obtaining and maintaining surface stability. CF‐FAB MS/MS spectra for several drugs are presented, including penicillin G, phentolamine, cocaine and benzoylecgonine. Minimum detection limits range from 50–500 pg injected, depending on the compound. The reproducibility of the integrated areas of peaks from repetitive injections is approximately five per cent. Data are also presented for the direct CF–FAB MS/MS analysis of cocaine and benzoylecgonine in spiked urine samples.
Oligopeptide sequence analysis by collision‐activated dissociation of multiply charged ions
Authors: Hunt Donald F. , Zhu Nian‐Zhou , Shabanowitz Jeffrey , Cooks R. G. 
Published: May 2005

AbstractCollision‐activated dissociation of an [M + 2H]2+ ion from a tryptic peptide of molecular weight 2315.3 provides sets of overlapping fragments that allow the amino acid sequence of this peptide to be determined on a triple quadrupole mass spectrometer having a mass range of 1800 Da.
Experimental determination of the double‐ionization energies of the trihalomethanes CF2ClH and CFCl2H
Authors: Griffiths W. J. , Harris F. M. 
Published: May 2005

AbstractThe double‐ionization energies of CF2ClH and CFCl2H have been measured by double‐charge‐transfer spectro‐scopy and are 33.1±0.5 eV and 30.3±0.5 eV, respectively. These values are smaller than the double‐ionization energy of CF3H and larger than the double‐ionization energy of CCl3H and thus exhibit the expected decrease as the fluorine atoms are replaced successively by chlorine atoms. This trend reflects a similar trend in the singleionization energies since for all the molecules the ratio of double‐ to single‐ionization energy lies between 2.5 and 2.6.
Determination of lovastatin acid in serum by gas chromatography/mass spectrometry
Authors: Wang‐Iverson David , Ivashkiv Eugene , Jemal Mohammed , Cohen Allen I. 
Published: May 2005

AbstractThe acid form of lovastatin, an HMG‐CoA reductase inhibitor, was analyzed by gas chromatography/negativeion chemical ionization mass spectrometry after derivatization with pentafluorobenzyl bromide and bis‐(trimethylsilyl)trifluoroacetamide (BSTFA). Mass spectrometry of this derivative produced a dominant [M–181]− ion under chemical ionization conditions using ammonia as the reagent gas. The limit of detection was approximately 2 pg injected on column.
Quantitation by fast‐atom bombardment/mass‐analysed ion kinetic energy spectrometry: Kinetic analysis of cyclic nucleotide phosphodiesterase activity
Authors: Newton R. P. , Walton T. J. , Brenton A. G. , Kingston E. E. , Harris F. M. 
Published: May 2005

AbstractQuantitation of cyclic nucleotide phosphodiesterase activity by means of fast‐atom bombardment (FAB) mass spectrometry with mass‐analysed ion kinetic energy (MIKE) spectrum scanning is described. Characteristic peaks of the substrate, cyclic AMP, and product, AMP, were identified in positive‐ion FAB mass spectra and MIKE scans of the protonated molecules. By spiking enzyme incubates with known quantities of cyclic AMP and AMP and measuring peak heights in the MIKE spectra of both spiked and unspiked samples, the concentrations of cyclic AMP and AMP in solution at the end of a series of enzyme incubations have been estimated. From the data obtained the Km and Vmax of the enzymes were calculated as 181 μM and 28.6 nmol/min respectively, showing excellent agreement with values of the Michaelis constant, Km=205 μM and the maximum velocity Vmax=33.2 nmol/min obtained by radioactive assay.
Compensation for non‐normal ejection of large molecular ions in plasma‐desorption mass spectrometry
Authors: Jonsson G. , Hedin A. , Håkansson Per , Sundqvist B. U. R. , Bennich H. , Roepstorff P. 
Published: May 2005

AbstractBy introducing an Einzel lens in the field‐free region of a straight time‐of‐flight mass spectrometer, secondary ions of large mass can be detected more efficiently in plasma‐desorption mass spectrometry. This procedure compensates for the large radial velocities of large molecular ions recently observed experimentally. It is shown that large molecular ions like those of lysozyme can now be detected more efficiently, and larger molecular ions than observed before in plasma‐desorption mass spectrometry (like those of bovine ovalbumin, mol. wt 45 000) can now be studied.
Negative‐ion mass spectrometry of substituted adenine bases and adenosine nucleosides
Authors: Hocart Charles H. , Schlunegger Urs P. 
Published: May 2005

AbstractThe negative‐ion chemical ionization (ammonia, 5 Pa source pressure) mass spectra of a series of substituted adenine bases, adenosine nucleosides, and the trimethylsilyl derivatives of the nucleosides are described. Selected ions from these spectra were subject to collisionally activated dissociation with mass‐analysed ion kinetic energy (CAD/MIKE) analysis of the products and the spectra assessed for information content. In addition to observing strong peaks due to quasimolecular ions and heterocyclic‐base ions, it proved possible to differentiate between 2′‐, 3′‐ and 5′‐deoxy and between 2′‐ and 3′‐O‐methyl isomers. The negative‐ion chemical ionization spectra of four methyladenines are essentially identical, but could be clearly distinguished from each other by CAD/MIKE analysis.
Competitive isomerization processes of 5‐methyl‐2‐hexanone radical cations
Authors: Audier H. E. , Denhez J. P. , Mourgues P. 
Published: May 2005

AbstractLabelled derivatives of the 5‐methyl‐2‐hexanone radical cation have permitted the elucidation of the origin of the main fragment ion [MC2H5]+ and the characterization of different rearrangement processes.
Experimental determination of the single‐ionization energies of two environmentally important free radicals, CF2Cl˙ and CFCl2˙
Authors: Griffiths W. J. , Harris F. M. , Barton J. D. 
Published: May 2005

AbstractThe single‐ionization energies of the free radicals CF2Cl˙ and CFCI2˙ have been measured by double‐charge‐transfer spectroscopy. The values obtained were 9.0 ± 0.5 eV and 8.5 ± 0.5 eV for CF2Cl˙ and CFCl2˙, respectively.
Fast‐atom bombardment mass spectrometry of conjugated benzo(a)pyrene metabolites
Authors: Greaves J. , Bieri R. H. 
Published: May 2005

AbstractFast‐atom bombardment mass spectrometry has been used to obtain spectra of conjugated benzo(a)pyrene (bap) metabolites using a 1:1, glycerol+thioglycerol matrix. bap Glucuronides give positive‐and negative‐ion spectra with peaks due to [M + H]+ and [M − H]− ions and a Major fragment peak (base peak) at [bapOH]+ and [bapO]−. bap Sulfates (sodium salts) give similar negative‐ion spectra with [M − Na]− and [bapO]− peaks, but the positive‐ion spectra are dominated by sodium and glycerol adducts of the bap sulfates.