bluuebunny/crossref_metadata_2025_split huggingface dataset:
Secondary structural features of modules M2 and M3 of barnase in solution by NMR experiment and distance geometry calculation
Authors: Ikura Teikichi , Gō Nobuhiro , Kohda Daisuke , Inagaki Fuyuhiko , Yanagawa Hiroshi , Kawabata Masuyo , Kawabata Shun‐ichiro , Iwanaga Sadaaki , Noguti Tosiyuki , Gō Mitiko 
Published: May 2005

AbstractProteins consist of structural units such as globular domains, secondary structures, and modules. Modules were originally defined by partitioning a globular domain into compact regions, each of which is a contiguous polypeptide segment having a compact conformation. Since modules show close correlations with the intron positions of genes, they are regarded as primordial polypeptide pieces encoded by exons and shuffled, leading to yield new combination of them in early biological evolution. Do modules maintain their native conformations in solution when they are excised at their boundaries? In order to find answers to this question, we have synthesized modules of barnase, one of the bacterial RNases, and studied the solution structures of modules M2 (amino acid residues 24–52) and M3 (52–73) by 2D NMR studies. Some local secondary structures, α‐helix, and β‐turns in M2 and β‐turns in M3, were observed in the modules at the similar positions to those in the intact barnase but the overall state seems to be in a mixture of random and native conformations. The present result shows that the excised modules have propensity to form similar secondary structures to those of the intact barnase. © 1993 Wiley‐Liss, Inc.
Molecular dynamics study of structure and stability of a model coiled coil
Authors: Zhang Li , Hermans Jan 
Published: May 2005

AbstractThis paper employs methods used earlier to study helix propensity in a model α‐helix. The methods are extended to simulations of a motif structure of the α‐helical coiled coil, i.e., a structure with a simple amino acid sequence, containing only alanine, leucine, and valine, with leucine and valine forming hydrophobic contacts in the helix interface (positions “d” and “a”). Dynamic simulations of the model coiled‐coil structure reproduce characteristic features of the coiled‐coil motif seen in experimental studies. Free energy simulations were used to assess the change in stability of the model when a leucine pair or a valine pair in the helix interface was replaced with an alanine pair. A leucine pair at position d was found to contribute 3.4 kcal/mol to the stability of the coiled coil relative to an alanine pair, and a valine pair at postion a was found to contribute 0.8 kcal/mol relative to an alanine pair. The value for the leucine pair agrees with reports in two experimental studies with molecules having different amino sequence. The value for the valine pair is reasonable given the smaller size of the valine side chain and the intrinsic low helix propensity of valine. No experimental value was available for comparison. © 1993 Wiley‐Liss, Inc.
A hypothetical complex between crystalline flavocytochrome b2 and Cytochrome c
Authors: Tegoni Mariella , White Scott A. , Roussel Alain , Mathews F. Scott , Cambillau Christian 
Published: May 2005

AbstractFlavocytochrome b2 and cytochrome c are physiological electron transfer partners in yeast mitochondria. The formation of a stable complex between them has been demonstrated both in solution and in the crystalline state. On the basis of the three‐dimensional structures, using molecular modeling and energy minimization, we have generated a hypothetical model for the interaction of these redox partners in the crystal lattice. General criteria such as good charge and surface complementarity, plausible orientation, and separation distance of the prosthetic groups, as well as more specific criteria such as the stoichiometry determined in the crystal, and the involvement of both domains and of more than one subunit of flavocytochrome b2 led us to discriminate between several possible interaction sites. In the hypothetical model we present, four cytochrome c molecules interact with a tetramer of flavocytochrome b2. The b2 and c hemes are coplanar, with an edge‐to‐edge distance of 14 Å. the contact surface area is ca. 800 Å2. Several electrostatic interactions involving the flavin and the heme domains of flavocytochrome b2 stabilize the binding of cytochrome c. © 1993 Wiley‐Liss, Inc.
Normal mode analysis of mouse epidermal growth factor: Characterization of the harmonic motion
Authors: Ikura Teikichi , Gō Nobuhiro 
Published: May 2005

AbstractNormal mode analysis of mouse epidermal growth factor (mEGF) has been carried out at room temperature. The value of the lowest frequency is 4.1 cm−1. This mode corresponds to hinge‐bending motion between the N‐terminal and C‐terminal domains of mEGF. This hinge‐bending motion corresponds to the “mitten mode.” In this motion, the N‐terminal domain is almost rigid. However, the C‐terminal domain is found to consist of three rigid segments. Two segments, C33‐D46 and G51‐R53, are observed moving in the same direction, but L47‐W50 moves in the opposite direction. For this mode, the effective Young's modulus turned out to be 1.1 × 109 dyn·−2. This value is a little larger than that of the mode with the lowest frequency 4.4 cm−1 of BPTI. The difference may be related to the fraction of residues involved in β‐sheets in the molecule. Similar analyses are carried out for other low frequency modes.
A monoclonal antibody fab fragment crystallized with and without a peptide epitope from HIV
Authors: Pfeffer‐Hennig Sabine , Wessner Helga , Hennig Michael , Dauter Zbigniew , Hausdorf Gert , Höhne Wolfgang E. 
Published: May 2005

AbstractThe Fab fragment of CB 4‐1, a monoclonal murine antibody against HIV protein p24, has been produced. It forms a complex with a synthetic antigen, an epitope of p24 made up of 11 amino acids, with the binding constant kd = 3.6 × 10−9 M. Crystals of hexagonal and orthorhombic space group has been obtained by cocrystallization of the Fab with the epitope and crystallization without the epitope, respectively. In either case, the crystals are suitable for X‐ray structural analysis. Crystals of the Fab fragment cocrystallized with the peptide have the space group P 6322 with cell dimensions of a = b = 105 Å, c = 297 Å. Fab crystals without the epitope are in space group C 222 with cell dimensions a = 110.1 Å, b = 110.2 c Å = 150.1 Å. © 1993 Wiley‐Liss, Inc.
Modeling the role of disulfide bonds in protein folding: Entropic barriers and pathways
Authors: Camacho Carlos J. , Thirumalai D. 
Published: May 2005

AbstractThe role of disulfide bonds in directing protein folding is studied using lattice models. We find that the stability and the specificity of the disulfide bond interactions play quite different roles in the folding process: Under some conditions, the stability decreases the overall rate of folding; the specificity, however, by yielding a simpler connectivity of intermediates, always increases the rate of folding. This conclusion is intimately related to the selection mechanism entailed by entropic driving forces, such as the loop formation probability, and entropic barriers separating the native and the many native‐like metastable states. The folding time is found to be a minimum for a certain range of the effective disulfide bond interaction. Examination of a model, which allows for the formation of disulfide bonded intermediates, suggests that folding proceeds via a threestage multiple pathways kinetics. We show that there are pathways to the native state involving only native‐like intermediates, as well as those that are mediated by nonnative intermediates. These findings are interpreted in terms of the appropriate energy landscape describing the barriers connecting low energy conformations. The consistency of our conclusions with several experimental studies is also discussed. © 1995 Wiley‐Liss, Inc.
The essential dynamics of thermolysin: Confirmation of the hinge‐bending motion and comparison of simulations in vacuum and water
Authors: van Aalten D. M. F. , Amadei A. , Linssen A. B. M. , Eijsink V. G. H. , Vriend G. , Berendsen H. J. C. 
Published: May 2005

AbstractComparisons of the crystal structures of thermolysin and the thermolysin‐like protease produced by B. cereus have recently led to the hypothesis that neutral proteases undergo a hinge‐bending motion. We have investigated this hypothesis by analyzing molecular dynamics simulations of thermolysin in vacuum and water, using the essential dynamics method. This method is able to extract large concerted atomic motions of biological importance from a molecular dynamics trajectory. The analysis of the thermolysin trajectories indeed revealed a large rigid body hinge‐bending motion of the Nterminal and C‐terminal domains, similar to the motion hypothesized from the crystal structure comparisons. In addition, it appeared that the essential dynamics properties derived from the vacuum simulation were similar to those derived from the solvent simulation. © 1995 Wiley‐Liss, Inc.
Laser microprobe fourier transform mass spectrometry. Preliminary results for feasibility and evaluation
Authors: Pelletier M. , Kreier G. , Muller J. F. , Weil D. , Johnston M. , MarshalI A. G. 
Published: May 2005

AbstractThe feasibility is reported of coupling a laser microprobe sampling system with a Fourier transform mass spectrometer (FTMS) for surface characterization. Analysis of an integrated circuit chip demonstrates capabilities for focusing the laser on a selected spot on a sample surface. Analysis of a model glass sample for which high resolution is required to separate metal ions from metal oxide ions emphasizes the advantages of coupling such a sampling system to an FTMS instrument.
Differentiation of type 1 and type 2 chain linkages of native glycosphingolipids by positive‐ion fast‐atom bombardment mass spectrometry with collision‐induced dissociation and linked scanning
Authors: Salyan Mary Ellen K. , Stroud Mark R. , Baillie T. A. , Levery Steven B. 
Published: May 2005

AbstractTwo underivatized glycosphingolipids, Leb and Ley, isomeric in carbohydrate structure (Fucα1 → 2Galβ1 → 3[Fucα1 → 4]GlcNAcβ1 → 3Glcβ1 → 4Glcβ1 → 1Cer and Fucα1 → 2Galβ1 → 4[Fucα1 → 3]GlcNAcβ1 → 3Galβ1 → 4Glcβ1 → 1Cer, respectively), were analyzed by positive‐ion fast‐atom bombardment (FAB) mass spectrometry with high energy collision‐induced dissociation (CID) and linked scanning. The two isomers were distinguishable by the abundance of product ions derived from the non‐reducing terminal tetrasaccharide fragment via sequential β‐eliminations of vivinaliy linked saccharide residues. Following earlier studies from other laboratories, which have dealt primarily with positive‐ion FAB‐CID mass spectrometry of simple model oligosaccharides, these results exemplify the practical application of two‐sector methodology to underivatized complex glycoconjugates commonly encountered in the biomedical field.
Analysis of peptides and proteins by capillary electrophoresis/mass spectrometry using acidic buffers and coated capillaries
Authors: Thibault P. , Paris C. , Pleasance S. , Caprioli R. M. 
Published: May 2005

AbstractThe direct coupling of capillary electrophoresis (CE) and mass spectrometry, combined with ionspray ionization using a coaxial capillary arrangement, is described. The CE/mass spectrometer interface is shown to be effective for the analysis of native and tryptic peptides and of proteins of high molecular weight such as bovine serum apotransferrin ( ≈78kDa). Adsorption of cationic analytes under acidic buffer conditions is minimized through the use of a non‐covalent coated capillary possessing an overall positive charge. Since the direction of the electroosmotic flow is thus reversed, compared to that in conventional CE separation on uncoated capillaries, migration of cations is achieved by applying a negative voltage (typically − 30kV) at the injector end of the capillary. In addition to the inherent advantage of providing pre‐formed cationic species for mass spectral detection, this arrangement permits analysis of proteins of high isoelectric points even at low pH. The ability to conduct electrophoesis of globular proteins under acidic conditions also provides a means of monitoring their conformational changes, as reflected both by the variation of migration times and by concurrent changes in the multiply charged ion envelopes.
Positive‐ion fast‐atom bombardment mass spectrometry of nitrogen macrocycles
Authors: Aubagnac J.‐L. , Marzin C. , Tarrago G. 
Published: May 2005

AbstractFast‐atom bombardment (FAB) mass Spectra of nitrogen macrocycles studied in this work show fragmentations which occur by loss of neutral molecules from the protonated molelcule to give even‐electron ions. Furthermore, both the neutral molecules and the even‐electron ions characterize substructures of each compound studied. Thus, it is easy to identify an unknown nitrogen macrocycle from its FAB mass Spectrum.
The electron affinity of UO3
Authors: Rudnyi E. B. , Kaibicheva E. A. , Sidorov L. N. 
Published: May 2005

AbstractThe ion/molecule equilibria method was applied to study negative ions while U3O8 was being vaporized. No UO opms were found. This has led to the conclusion that the electron affinity (EA) of UO3 is less than 205kJ mol−1, in complete contradiction to Gurvich's prediction that EA(UO3)=500±50kJ mol−1.
Analysis by a combination of gas chromatography and tandem mass spectrometry: Development of quantitative tandem‐in‐time ion trap mass spectrometry: Isotope dilution quantification of 11‐nor‐delta‐9‐tetrahydrocannabinol‐9‐carboxylic acid
Authors: Phinney Curtis S. , Welch Michael J. 
Published: May 2005

AbstractCollision‐induced dissociation (CID) was performed in an ion‐trap mass spectrometer to investigate quantification by isotope dilution and gas Chromatography coupled with tandem mass spectrometry (GC/MS/MS). The operating system software was modified to allow simutaneous CID of two ions differing only slightly in mass/ charge ratios. Simultaneous excitation of the base peaks of the parent compound and its deuterated analog in a co‐eluting GC peak leads to quantitative and reproducible formation of daughter ions. Changing conditions in the mass analyzer as the GC peak elutes required broadening of the CID excitation frequency pattern. This had to be done so that relatively uniform dissociation energy would be imparted to both parent ions during the concentration changes associated with the elution of a GC peak. A commonly measured human metabolite of marijuana, 11‐nor‐delta‐9‐tetrahydrocannabinol‐9‐carboxylic acid, was analyzed in freeze‐dried urine. The mean value, 14.0±0.61 (1 standard deviation) ng/mL, agrees very well with the GC/MS mean measured value of 14.1±0.45 ng/mL. The overall coefficient of variation for the individual ion‐trap MS/MS sample measurements is 4.3%.
Quantitative attenuated total reflection (ATR) spectroscopy of films with an absorption gradient
Authors: Stuchebryukov S. D. , Vavkushevsky A. A. , Rudoy V. M. 
Published: May 2005

AbstractA method for quantitatively studying the absorption gradients in films of a thickness of an incident radiation wavelength, by means of attenuated total reflection (ATR) spectroscopy is proposed. The possibilities and limitations of the method are discussed.
A practical method for determining backscattering factors and matrix correction in quantitative aes analysis of binary alloys
Authors: Streubel Peter , Berndt Helga 
Published: May 2005

AbstractThe composition‐dependent backscattering factor in quantitative AES analysis is investigated by comparing experimental results from different approaches with several theoretical methods. Backscattering factor ratios are presented as a function of the composition of homogeneous CuPd alloys cleaned in situ by scribing. The values were calculated in a simple way by the proposed approximation method which takes into account the importance of the primary electron incident angle. This approach can be recommended for practical use in determining matrix correction. Application of the approximation method for matrix correction to different binary alloy systems gives a better agreement with the experimental matrix correction factor than Reuter's backscattering factor equation. Matrix correction factors for binary alloys were evaluated by a simple equation considering the weak linear composition dependence which was found experimentally. With matrix correction the accuracy of quantitative AES analysis can be improved by 5% or more as was shown for the CuPd alloys.
XPS: Energy calibration of electron spectrometers. 2—Results of an interlaboratory comparison
Authors: Anthony M. T. , Seah M. P. 
Published: May 2005

AbstractAn interlaboratory test of the NPL calibration values and methodology for the energy scale of XPS instruments, given in Part 1, has been completed. The NPL calibration values are given for the Cu 3p, Au 4f7/2, Ag 3d5/2, Cu LMM, Cu 2p3/2, and Ag MNN peaks for A1 and Mg Kα radiations to an accuracy of 20 me V. Thirteen participants reported with their values for these peaks from seven instrument models representative of four manufacturers. These results are analysed in terms of random errors, voltage scaling errors and zero offset errors. The random errors are the smallest of these errors and amount to 30 me V, showing that instrument users can assign peak positions with very high precision. However, the voltage scaling and zero errors range up to 700 ppm and 1363 me V respectively showing that the weakest link in the commercial measurement chains is in the electronics. It is not clear if this is mainly due to drift in the electronics after the manufacturer's installation or inadequte calibration at that time. A detailed analysis of the measurements confirms the linearity of each of the instrument energy scales to within the accuracy of their random errors.
Spatially multidimensional SIMS analysis
Authors: Rüdenauer F. G. 
Published: May 2005

AbstractA review of the instrumental development of spatially multidimensional elemental SIMS analysis is given. This new method makes use of fast image digitization, digital image storage and digital image processing techniques and is applicable to both scanning ion microprobes and ion microscopes. A variety of physical processes may produce image artifacts which distort image signal modulation, prevent correct spatial registration and relocate sample atoms in the interior of the sample from their original positions. Attempts at correction of these artifacts are described.
Quantitative XPS analysis considering elastic scattering
Authors: Ebel H. , Ebel M. F. , Wernisch J. , Jablonski A. 
Published: May 2005

AbstractUp to now the equations for both quantitative XPS analysis and those for the determination of reduced thicknesses of thin overlayers have been derived according to the assumption of a well‐defined photoelectron escape length. Escape length distributions are caused by a variety of influences. The consequences of this are demonstrated by the example of thin overlayers. Additionally, an approximation is developed which accounts for elastic electron scattering. The ratio Λ/λel of mean free path is the characteristic quantity of this approximation, which is quantified by comparison of Monte Carlo calculations and thin film experiments. This approximation allows us to conclude that elastic electron scattering does not influence quantitative XPS analysis, so long as it is performed without any kind of references.
Observation of CuNi alloy surfaces by low wattage glow discharge emission spectrometry
Authors: Wagatsuma Kazuaki , Hirokawa Kichinosuke 
Published: May 2005

AbstractGlow discharge sputtering on CuNi alloy surfaces is studied by optical emission spectroscopy and Auger electron spectroscopy. The relative intensity of Cu emission lines against Ni lines increases with a decrease in supplied power in very low wattage regions. These changes of the relative intensities principally depend on the sputtering parameters of constituent elements in CuNi alloy; that is, the preferential sputtering of copper. Surface analysis by Auger electron spectroscopy shows that when samples are sputtered by glow discharges in very low power operations, the deformation layer which has a nickel‐enriched composition exists on alloy surfaces. We discuss the effect of glow discharge sputterings on surface compositions using the two analytical methods described above.
Analytical application of XPS for surface characterization of coal fly ash and coal
Authors: Hirokawa K. , Danzaki Y. 
Published: May 2005

AbstractSurface observation of coal and coal ashes was performed by XPS. S, P and N in coal and coal fly ashes were especially noticed as environmental contaminating elements, S in SO type and P in PO type in fly ash, and S in thiophene type and oxide type, N in pyrrole and pyridine type in coal were found, respectively. The some S compounds in coal and fly ash, and N compounds in coal were dissolved in water by leaching, but P in fly ash remained in the residue as PO type.
Depth profiling on a sputtered bevel of sub‐degree slope angle
Authors: Gries W. H. 
Published: May 2005

AbstractA new method is described whereby a surface can be bevel‐sectioned by means of sputtering at a slope angle of any desired sharpness. In contrast with other proposals of sputter‐bevelling this method produces an elevated bevel section. Measurements on a shallow diffusion profile of boron in a silicon wafer using this method show the profile reproduction to be very satisfactory. Distorting effects on the projection of the depth profile on the sputtered bevel are discussed. Scanning Auger and ion microprobes are compared for their suitability for reproducing a depth profile from its projection on a sputtered bevel.
Scanning ion imaging as a diagnostic tool for an ion microscope
Authors: Brown J. D. , Vandervorst W. 
Published: May 2005

AbstractA scanning system has been installed on a Cameca IMS 3f ion microscope. The system has been invaluable for alignment of secondary ion extraction to the centre of the crater during depth profiling, detection of inclusions and lateral inhomogeneities during depth profiling and compensation of charging of insulators using an electron flood gun. Limitations of the standard gun have become apparent.
Stabilization of charge on electrically insulating surfaces during SIMS experiments—experimental and theoretical studies of the specimen isolation method
Authors: Lau W. M. , McIntyre N. S. , Metson J. B. , Cochrane D. , Brown J. D. 
Published: May 2005

AbstractRecent experiments have shown that secondary ion mass spectrometric (SIMS) measurements of insulator surfaces can be greatly facilitated by the use of a charged aperture located immediately above the analysis area (the ‘specimen isolation technique’). This allows the surface potential within the aperture area to be stabilized. Charging is stabilized when the potential difference between the surface and the aperture becomes large enough that excessive charge, in the form of secondary electrons, is drained away from the surface to the aperture. The potential difference generated on such insulating surfaces can be measured experimentally by varying the voltages applied to the electrostatic analyzer to measure the secondary ion intensity as a function of kinetic energy. Such measurements have been carried out on a Cameca IMS‐3F instrument for a range of aperture dimensions and for different primary and secondary ions. The surface potential can be stabilized at a potential readily measurable by the electrostatic analyzer for both O− and Cs+ ion beams. The mechanism for this stabilization has been analyzed through calculations of two dimensional contours for the region around the specimen holder. For surfaces with a very high charging potential (>600 V), potential wells which can trap ions of low kinetic energy develop near the surface. Element and oxide secondary ion kinetic energy distribution curves, taken under specimen isolation conditions, which differ from those obtained under normal non‐charging SIMS conditions, are evidence for such ion trapping.