bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recurrent αβ loop structures in TIM barrel motifs show a distinct pattern of conserved structural features
Authors: Scheerlinck Jean‐Pierre Y. , Lasters Ignace , Claessens Michel , De Maeyer Marc , Pio Frederic , Delhaise Philippe , Wodak Shoshana J. 
Published: May 2005

AbstractA systematic survey of seven parallel α/β barrel protein domains, based on exhaustive structural comparisons, reveals that a sizable proportion of the αβ loops in these proteins—20 out of a total of 49—belong to either one of two loop types previously described by Thornton and co‐workers. Six loops are of the αβ1 type, with one residue between the α‐helix and β‐strand, and 13 are of the αβ3 type, with three residues between the helix and the strand. Protein fragments embedding the identified loops, and termed αβ connections since they contain parts of the flanking helix and strand, have been analyzed in detail revealing that each type of connection has a distinct set of conserved structural features. The orientation of the β‐strand relative to the helix and loop portions is different owing to a very localized difference in backbone conformation. In αβ1 connections, the chain enters the β‐strand via a residue adopting an extended conformation, while in αβ3 it does so via a residue in a near α‐helical conformation. Other conserved structural features include distinct patterns of side chain orientation relative to the β‐sheet surface and of main chain H‐bonds in the loop and the β‐strand moieties. Significant differences also occur in packing interactions of conserved hydrophobic residues situated in the last turn of the helix. Yet the α‐helix surface of both types of connections adopts similar orientations relative to the barrel sheet surface. Our results suggest furthermore that conserved hydrophobic residues along the sequence of the connections, may be correlated more with specific patterns of interactions made with neighboring helices and sheet strands than with helix/strand packing within the connection itself. A number of intriguing observations are also made on the distribution of the identified αβ1 and αβ3 loops within the α/β‐barrel motifs. They often occur adjacent to each other; αβ3 loops invariably involve even numbered β‐strands, while αβ1 loops involve preferentially odd β‐strands; all the analyzed proteins contain at least one αβ3 loop in the first half of the eightfold α/β barrel. Possible origins of all these observations, and their relevance to the stability and folding of parallel α/β barrel. Possible origins of all these observations, and their relevance to the stability and folding of parallel α/β barrel motifs are discussed.
Conformational deformation in deoxymyoglobin by hydrostatic pressure
Authors: Yamato Takahisa , Higo Jun'ichi , Seno Yasunobu , Gō Nobuhiro 
Published: May 2005

AbstractPressure effect on the equilibrium conformation in sperm whale deoxymyoglobin and its volume fluctuation are studied by the normal mode analysis and strain tensor analysis. The pressure‐induced deformation of interhelix regions are found to be remarkably more compressed than the other parts of the molecule. The intrahelix compressibility is shown to be relatively small. We also calculate the compressibility of the three hydrophobic clusters, located at the bottom, distal, and proximal side of the heme. Its value is found to decrease in the indicated order. The average compressibility of these hydrophobic clusters is less than the average interhelix compressibility, even though there are large cavities in these clusters. In order to study overall deformation, we define a linear compressibility and calculate it for all pairs of Cαatoms. The pressure‐induced deformation is observed to be heterogeneous also in this analysis. The calculated root‐mean‐square displacement of the constituent atoms in the equilibrium conformation at 1,000 atm from those at 0 atm is 0.12 Å, which is much smaller in magnitude than the average value of the atomic fluctuations at room temperature. In the water solvent, the volume excluded by the protein molecule in the equilibrium conformation is reduced by 0.9%, when the pressure is raised from 0 to 1,000 atm. The calculated magnitude of the root‐mean‐square volume fluctuation is 0.3% of the excluded volume at room temperature. The square of the volume fluctuation is given as a sum of contributions from individual normal modes. Contributions from low frequency normal modes are found to dominate over those from higher frequency normal modes. The estimated value of the isothermal compressibility of deoxymyoglobin is 9.37 × 10−12 cm2/dyn. © 1993 Wiley‐Liss, Inc.
Crystal structure of Escherichia coli TEM1 β‐lactamase at 1.8 Å resolution
Authors: Jelsch Christian , Mourey Lionel , Masson Jean‐Michel , Samama Jean‐Pierre 
Published: May 2005

AbstractThe X‐ray structure of Escherichia coli TEM1β‐lactamase has been refined to a crystallorgphic R‐factor of 16.4% for 22,510 reflections between 5.0 and 1.8 Å resolution; 199 water molecules and 1 sulphate ion were included in refinement. Except for the tips of a few solvent‐exposed side chains, all protein atoms have clear electron density and refined to an average atomic temperature factor of 11 Å2. The estimated coordinates error is 0.17 Å. The substrate binding site is located at the interface of the two domains of the protein and contains 4 water molecules and the sulphate anion. One of these solvent molecules is found at hydrogen bond distance from S70 and E166. S70 and S130 are hydrogen bonded to K73 and K234, respectively. It was found that the E. coli TEM1 and Staphylococcus aureus PC1 β‐lactamases crystal structures differ in the relative orientations of the two domains composing the enzymes, which result in a narrowed substrate binding cavity in the TEM1 enzyme. Local but significant differences in the vicinity of this site may explain the occurrence of TEM1 natural mutants with extended substrate specificities. © 1993 Wiley‐Liss, Inc.
Continuous measurement of water in organic solution by membrane‐inlet mass spectrometry
Authors: Bohátka Sándor , Degn Hans 
Published: May 2005

AbstractWith a membrane made of a relatively polar material, membrane‐inlet mass spectrometry can be used to measure the water activity in organic liquids of low dielectric constant. The detection limit for water depends on the solubility of water in the organic liquid. In butanol, hexanol, octanol and octane the detection limits at 45°C are 7, 4, 3 and 0.3 ppm, respectively. The half‐time of the water reponse at 45°C is 20 s. The method can be used for continuous monitoring of water in reaction systems in organic solvents. Examples given are the condensation of 2,4‐dimethyl‐3‐pentanone with phenylhydrazine in hexanol solution and the hydrolysis of acetylchloride in octane solution.
Specific reactivity of the ‘magic bullet’ matrix in the negative‐ion fast‐atom bombardment mass spectra of organic anions
Authors: Aubagnac Jean‐Louis , Man Michel Wong Chi , Elguero José 
Published: May 2005

AbstractThe magic bullet matrix shows a noticeable and specific reactivity towards two organometallic anions (borate and silicate). Thus, before selecting this matrix to study organic salts by fast‐atom bombardment mass spectrometry, it is necessary to check for this specific reactivity.
Negative‐ion mass spectra of methylated diuretics
Authors: Ehrhardt J. D. 
Published: May 2005

AbstractThe negative‐ion mass spectra of 19 methylated diuretics are presented and correlations between these spectra and the chemical structures of the compounds are indicated. The spectra are of interest as the basis of an anylytical method for the identification of small quantities of diuretics in the urine of hypokalemic patients.
Study of water–cryoprotector mixtures by low temperature fast‐atom bombardment mass spectrometry
Authors: Boryak Oleg A. , Kosevich Marina V. , Shelkovsky Vadim S. , Blagoy Yurii P. 
Published: May 2005

AbstractFrozen solutions of a cryoprotector, glycerol, in water were studied by low temperature fast‐atom bombardment mass spectrometry in the temperature range from − 196° to 0°C. Strong dependence of the mass spectral pattern on the water‐glycerol ratio and temperature of the sample was observed. The evolution of mass spectra of the frozen 2000:1 water‐glycerol mixture with increase of the sample temperature is reproducible: in the lower portion of the temperature range (−196° to −120°C) the spectra contain a set of cluster ions, (H2O)nH+, (n = 1–15), characteristic of pure water; then the spectra show a superposition of peaks due to water clusters and glycerol itself, the latter with characteristic changes with temperature rise: degraded ‘peak at every mass’ pattern in the −120° to −80°C range followed by a build‐up of glycerol clusters, GnH+, (n = 1–3) in the −80°C to −55°C range. At approximately −55°C to −50°C a sublimation of water component occurs, detected by [H2O]+· ion, and the remainder of the spectral pattern coincides with that of pure glycerol up to ambient temperature. Mixed water‐glycerol clusters were never observed. An explanation of such spectral behavior is proposed based on ideas about the morphology of the frozen solutions, characterized by water microcrystallites separated by eutectic channels containing cryoprotector. The independent sputtering of the two substances from different domains of the frozen sample surface is discussed.
‘On‐line’ liquid chromatography/nuclear magnetic resonance mass spectrometry—a powerful spectroscopic tool for the analysis of mixtures of pharmaceutical interest
Authors: Pullen Frank S. , Swanson Alistair G. , Newman Michael J. , Richards Don S. 
Published: May 2005

AbstractLiquid chromatography (LC), simultaneously coupled with both nuclear magnetic resonance (NMR) and mass spectrometry (MS) ‘on‐line’ is a powerful structural tool and has a potentially vast range of uses within the pharmaceutical industry. Data from a mixture of fluconazole and related triazoles have been obtained from an LC/NMR‐MS system developed ‘in‐house’, demonstrating the power of this novel analytical approach.
Multiresidue determination of quinolone antibiotics using liquid chromatography coupled to atmospheric‐pressure chemical ionization mass spectrometry and tandem mass spectrometry
Authors: Doerge Daniel R. , Bajic Steve 
Published: May 2005

AbstractLiquid chromatography coupled to atmospheric‐pressure chemical ionization mass spectrometry and tandem mass spectrometry (MS/MS) methods for the determination and quantification of four quinolone antibiotics were adapted from a published procedure for liquid‐liquid extraction from catfish muscle and high‐performance liquid chromatographic analysis. In‐source collision‐induced dissociation was used to optimize fragmentation to produce mass spectra consisting of the protonated molecule and two characteristic fragment ions of nearly equal intensity. Selected ion monitoring of three ions per quinolone yielded sensitive detection in catfish muscle extracts (estimated instrumental detection limits 0.8‐1.7 ppb). The intensity ratios were used to confirm the presence of three of the quinolones based on the accurate agreement (⩽10% deviation) between ratios derived from fortified catfish extracts and those from standard quinolones. MS/MS was used to increase the specificity and sensitivity of analysis. Scans using constant neural loss (CNL) of 18 mass units gave a sensitive response for the quinolones suggesting that CNL scans may be applicable to multiresidue screening for unknown quinolones. MS/MS with multiple reaction monitoring of the [MH18]+ transition for each quinolone yielded the highest sensitivity analysis in catfish extracts (estimated instrumental detection limits 0.08–0.16 ppb).
Reverse isotope dilution analysis of 13CO2 using gas chromatography/isotope ratio mass spectrometry: Application to the quantitative determination of 13CO2 released by human polymorphonuclear leukocytes
Authors: Lamrini Rachid , Lacan Philippe , Francina Alain , Guilluy Roger , Brazier Jean Louis 
Published: May 2005

AbstractWe propose a new method for the quantitative determination of carbon dioxide released by a biological microgenerator: a suspension of human polymorphonuclear leukocytes (PMNL). This method is based on the reverse isotope dilution analysis by gas chromatography/isotope ratio mass spectrometry of 13CO2 released by PMNL in a controlled isotope abundance atmosphere containing 3% CO2.13CO2 release is effective after PMNL stimulation in the presence of [13C]glucose, labeled on positions 1, 2 or 6. The validation of this method is carried out by the measurement of the isotope ratio 13CO2/12CO2 using known amounts of [13C]sodium hydrogen carbonate and the comparison with theoretical isotope abundances derived from various CO2 equilibria. Complete release of CO2 is achieved by the acidification of the medium. This method requires only few cells, displays high sensitivity and specificity and can be applied to the analysis of large series of samples using an automatic sample injector. In addition, this method can also be applied to other types of biological microgenerators of carbon dioxide.
Electrospray mass spectrometric characterization of fluoroquinolone antibiotics: Norfloxacin, enoxacin, ciprofloxacin and ofloxacin
Authors: D'Agostino Paul A. , Hancock James R. , Provost Lionel R. 
Published: May 2005

AbstractWe report the electrospray (ESI) mass spectra of four fluoroquinolones, enoxacin, norfloxacin, ofloxacin and ciprofloxacin, a group of highly potent antibiotics that have not been previously characterized by this ionization technique. At low sampling cone voltage settings, 50 and 100 V, the electrospray mass spectra contained primarily molecular adduct ions. At a sampling cone voltage setting of 150 V, collisionally activated dissociation mass spectra containing structurally significant product ions were produced and accurately mass measured at a magnetic sector resolution of 3000. Gradient separation and characterization of these compounds was demonstrated by analysis using packed capillary column liquid chromatography with UV and ESI‐MS detection. UV detection limits in the 1 to 2 ng range ((signal‐to‐noise ratio S/N) = 10:1) were estimated and interpretable mass spectra with S/N ratios in excess of 100:1 were observed for 1.5 ng of analyte during electrospray mass spectrometric analysis.
Sequencing electroblotted proteins by tandem mass spectrometry
Authors: Fabris D. , Vestling M. M. , Fenselau C. , Cordero M. M. , Doroshenko V. M. , Cotter R. J. 
Published: May 2005

AbstractElectroblotting proteins separated by gel electrophoresis provides a suitable support for further manipulations and analysis of small amounts of relatively pure samples. On‐membrane digestion, peptide mapping by mass spectrometry, and database searching offer sensitive and fast tools to identify the analyte. By providing sequence information, tandem mass spectrometry can go a step further, confirming the database identification, solving problems connected with post‐translational modifications and sequence variations, or supplying the stretches of internal sequence necessary to synthesize an oligonucleotide probe for gene isolation. The viability of this approach was successfully evaluated using different tandem mass spectrometric techniques: metastable decomposition in a matrix‐assisted laser desorption/ionization (MALDI) time‐of‐flight instrument with a curved‐field reflectron; low energy collision‐induced dissociation in a MALDI quadrupole ion trap mass spectrometer; and high energy collision‐induced dissociation in a high‐performance four‐sector mass spectrometer with massive cluster‐impact ionization.
Error‐tolerant protein database searching using peptide product‐ion spectra
Authors: Bonner Ron , Shushan Bori 
Published: May 2005

AbstractA method for matching proteins in databases with unknown samples using data derived from peptide production masses is described. The power of the method is due to the speed of analysis and to the ability to locate proteins in a database even when the experimental data show anomalies due to derivatization or post‐translational modification.
Characterization of fresh and spent HDS catalysts by Auger and X‐ray photoelectron spectroscopies
Authors: Brinen J. S. , Graham S. W. , Hammond J. S. , Paul D. F. 
Published: May 2005

AbstractHigh resolution scanning Auger measurements have been made of HDS catalysts recovered from a heavy oil refining operation. Element maps and Auger spectra point out spectral inhomogeneities existing on the used catalyst which hitherto have not been reported. Once charging has been controlled, the information obtained sheds a new dimension for the study of catalysts on insulating support materials.
Affinity of lead for noble metals on different supports
Authors: Gandhi H. S. , Williamson W. B. , Logothetis E. M. , Tabock J. , Peters C. , Hurley M. D. , Shelef M. 
Published: May 2005

AbstractDirect association of lead compounds with Pt, Pd and Rh sputtered onto ZrO2, TiO2 and Al2O3 wafer supports was observed. The samples were exposed to combustion products of iso‐octane containing 1.5 g Pb gal−1 as Motor Mix, 0.8 mg P gal−1 and 0.03 wt% S at 700°C in an overall lean exhaust; however, the samples experienced alternating rich and lean exhaust pulses. A semi‐quantitative electron microprobe study showed that the association of lead compounds to the surface of Pt, Pd and Rh was at least 2 or 3 orders of magnitude higher compared to the amount found on the supports. On Pt lead was present predominantly as PbSO4, on Rh as PbO or Pb metal, and as solid solution in Pd. These large differences in the form of Pb compounds could explain the known fact that Pd and Rh are more sensitive to Pb poisoning than Pt. The higher activity of Pt in catalyzing the oxidation of SO2 to SO3 results in the formation of stable but inert PbSO4 on Pt. On the other hand, Rh and Pd are poor catalysts for SO2 oxidation and therefore Pb remains as PbO or Pb on Rh and forms PdPb solid solutions with Pd. In both cases (Pd and Rh) the active sites for catalytic reactions are poisoned. Halide‐containing lead species were more specific than volatile PbO in poisoning noble metals as indicated by various independent experimental observations.
Application of X‐ray‐induced Auger electron spectroscopy to state analyses of hydrogen implanted in Y, Zr and Nb metals
Authors: Baba Yuji , Sasaki Teikichi A. 
Published: May 2005

AbstractX‐ray‐induced Auger electron spectroscopy (XAES) was used to examine the surface chemical states of hydrogen implanted metals. The chemical shifts of the M4,5N2,3V Auger peaks from their metallic states were 1.0 eV, 3.3 eV and 2.2 eV, respectively, for ion‐implanted Y, Zr and Nb. The separation energies were found to be much larger than those of the corresponding 3d5/2 lines in the XPS spectra.
Comparative study of ion implantation profiles in metals
Authors: Takadoum J. , Pivin J. C. , Pons‐Corbeau J. , Berneron R. , Charbonnier J. C. 
Published: May 2005

AbstractSecondary ion mass spectrometry and glow discharge optical spectrometry are used to determine the depth profiles of Ni and Fe matrices implanted with B and P. These measurements enable the emission yields of secondary ions (for SIMS) or photons (for GDOS) emitted under ion bombardment to be quantified and consequently the implanted samples can be used as standards. The profiles obtained by both methods are in good agreement and independant of the surface roughness. They are compared to real distributions determined by Rutherford backscattering (RBS) and to theoretical ones predicted by the model of Winterbon, Sigmund and Sanders; the concentrations measured at the maximum of the distribution are smaller then the theoretical ones and the experimental profiles are wider than those given by the theory. The causes of the alterations in the profiles are discussed and the surface contamination of the samples is studied by mean of GDOS profiles.
Analysis of polymer surfaces by SIMS. 4—A study of some acrylic homo‐ and co‐polymers
Authors: Briggs D. , Hearn M. J. , Ratner B. D. 
Published: May 2005

AbstractStatic SIMS spectra from essentially undamaged acrylic polymers have been obtained for total ions doses of 2 × 1012 ions cm−2. For a series of polymethacrylates the spectra can be interpreted in terms of a constant contribution from the polymer backbone plus dominant fragments from the ester side chain. Isomeric butyl methacrylate polymers can be distinguished. Negative ion spectra reflect the O:C atomic ratio of the bulk polymer. Positive ion relative intensities from ethyl methacrylate: hydroxyethyl methacrylate random copolymers correlate with polymer composition. Previous SIMS data from polymethacrylates have been shown to represent highly damaged surfaces.
Quantitative XPS: The calibration of spectrometer intensity—energy response functions. 2—Results of interlaboratory measurements for commercial instruments
Authors: Seah M. P. , Jones M. E. , Anthony M. T. 
Published: May 2005

AbstractAn interlaboratory experiment to establish X‐ray photoelectron spectrometer intensity–energy response functions has been completed. The measurements made by fifteen participants give results for seven instrument models from four manufacturers. Two methods of determining the response function are tested: (i) by peak area measurement and (ii) using the background data from wide scan spectra from reference foils of Cu, Ag and Au. The peak area data show excellent reproducibility, and area ratios, when corrected for instrument response functions, are consistent to a standard deviation of 4% for Ag and Au between all instruments and conditions. The response functions relative to the VG Scientific ESCA 3 Mk II are proportional to En where, in the constant ΔE mode, n = −;0.20±0.03 for the Leybold LHS10, −0.15±0.10 for the Perkin–Elmer PHI 550, 0.00±0.03 for the VG Scientific ESCA 3, and 0.20±0.02 for the VG Scientific ESCALAB I and II. The AEI/Kratos ES 200B/300 gives a complex, but defined, function. In the constant ΔE/E mode the latter instrument gives n in the range 1.3 to 2.0 and the VG Scientific ESCALAB II 1.79±0.05.
SIMS study of the penetration of metallic secondary impurities in screen‐printed silicon solar cells
Authors: Van Craen M. , Frisson L. , Adams F. C. 
Published: May 2005

AbstractThe penetration of metallic B, Ti, Fe, Cu and Ag in silicon solar cells was studied. They were prepared using the screen printing process for metallization. The level and depth of penetration were determined using secondary ion mass spectrometry (SIMS). Quantitative SIMS depth profile analysis was performed using ion implanted substrates as standard materials. The influence of different production parameters, such as silicon crystal orientation, metallization temperature, composition of the Ag‐paste and the presence of an anti‐reflective TiOx coating on the silicon cells were determined. The penetration of some metallic species has considerable influence on the solar cell characteristics and its efficiency. The penetration levels can not be explained by diffusion but are probably related to more reactive interactions.
Quantitative ISS/XPS measurements on HDS catalysts
Authors: Brinen J. S. , D'Avignon D. A. , Meyers E. A. , Deng P. T. , Behnken D. W. 
Published: May 2005

AbstractISS and XPS spectra were obtained for hydrodesulfurization (HDS) catalysts made by two different preparative methods. Quantitative XPS measurements were used with ISS depth profiles to demonstrate that quantitative ISS data could be obtained despite the irregular structure of catalyst surfaces. Atomic compositions as a function of depth were then obtained by (1) use of ISS data directly or (2) by XPS formalism using a non‐constant depth distribution.