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At least 1,063 records · Page 59

Crystallization and preliminary X-ray diffraction study of recombinant ribokinase from Thermus Species 2.9

Ribokinase from a thermophilic strain of Thermus species 2.9 belonging to the carbohydrate ribokinase family (EC 2.7.1.15) was isolated, purified, and crystallized. The crystallization conditions were found by the vapor-diffusion technique and were then optimized to apply the capillary counter-diffusion technique. The X-ray diffraction data set was collected from the crystals, which were grown by the counter-diffusion technique, at the SPring-8 synchrotron radiation facility to 2.87 Å resolution. The crystals belong to sp. gr. P12{sub 1}1 and have the following unit-cell parameters: a = 81.613 Å, b = 156.132 Å, c = 87.714 Å, α = γ = 90°, β = 103.819°. The X-ray diffraction data set is suitable for determining the three-dimensional structure of the protein by the molecular-replacement method.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Crystallization and preliminary X-ray diffraction study of recombinant adenine phosphoribosyltransferase from the thermophilic bacterium Thermus thermophilus strain HB27

Adenine phosphoribosyltransferase (APRT) belongs to the type I phosphoribosyltransferase family and catalyzes the formation of adenosine monophosphate via transfer of the 5-phosphoribosyl group from phosphoribosyl pyrophosphate to the nitrogen atom N9 of the adenine base. Proteins of this family are involved in a salvage pathway of nucleotide synthesis, thus providing purine base utilization and maintaining the optimal level of purine bases in the body. Adenine phosphoribosyltransferase from the extremely thermophilic Thermus thermophilus strain HB27 was produced using a highly efficient E. coli producer strain and was then purified by affinity and gel-filtration chromatography. This enzyme was successfully employed as a catalyst for the cascade biosynthesis of biologically important nucleotides. The screening of crystallization conditions for recombinant APRT from T. thermophilus HB27 was performed in order to determine the enzyme structure by X-ray diffraction. The crystallization conditions, which were found by the vapor-diffusion technique, were then optimized to apply the counter-diffusion technique. The crystals of the enzyme were grown by the capillary counter-diffusion method. The crystals belong to sp. gr. P12{sub 1}1 and have the following unitcell parameters: a = 69.86 Å, b = 82.16 Å, c = 91.39 Å, α = γ = 90°, β = 102.58°. The X-ray diffraction data set suitable for the determination of the APRT structure at 2.6 Å resolution was collected from the crystals at the SPring-8 synchrotron facility (Japan).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Purification, isolation, crystallization, and preliminary X-ray diffraction study of the BTB domain of the centrosomal protein 190 from Drosophila melanogaster

The spatial organization of the genome is controlled by a special class of architectural proteins, including proteins containing BTB domains that are able to dimerize or multimerize. The centrosomal protein 190 is one of such architectural proteins. The purification, crystallization, and preliminary X-ray diffraction study of the BTB domain of the centrosomal protein 190 are reported. The crystallization conditions were found by the vapor-diffusion technique. The crystals diffracted to 1.5 Å resolution and belonged to sp. gr. P322{sub 1}. The structure was solved by the molecular replacement method. The structure refinement is currently underway.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Preliminary small-angle X-ray scattering and X-ray diffraction studies of the BTB domain of lola protein from Drosophila melanogaster

The Drosophila genome has several dozens of transcription factors (TTK group) containing ВТВ domains assembled into octamers. The LOLA protein belongs to this family. The purification, crystallization, and preliminary X-ray diffraction and small-angle X-ray scattering (SAXS) studies of the BTB domain of this protein are reported. The crystallization conditions were found by the vapor-diffusion technique. A very low diffraction resolution (8.7 Å resolution) of the crystals was insufficient for the determination of the threedimensional structure of the BTB domain. The SAXS study demonstrated that the BTB domain of the LOLA protein exists as an octamer in solution.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Crystallization and Preliminary X-ray Diffraction Study of Purine Nucleoside Phosphorylase from the Thermophilic Bacterium Thermus thermophilus Strain HB27

Recombinant purine nucleoside phosphorylase from the thermophilic Thermus thermophilus strain encoded by the TT-C0194 gene was purified to homogeneity. The crystallization conditions for the enzyme were found by the vapor-diffusion technique. The crystals of the enzyme suitable for X-ray diffraction were grown under microgravity conditions by the capillary counter-diffusion method. The crystals belong to sp. gr. P2{sub 1}2{sub 1}2{sub 1} and have the following unit-cell parameters: a = 89.9 Å, b = 121.0 Å, c = 215.7 Å, α = β = γ = 90°. The X-ray diffraction data set suitable for the determination of the three-dimensional structure of purine nucleoside phosphorylase was collected from the grown crystals at the SPring-8 synchrotron facility to 2.5 Å resolution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Extremely asymmetric diffraction as a method of determining magneto-optical constants for X-rays near absorption edges

The spectral dependence of the Bragg peak position under conditions of extremely asymmetric diffraction has been analyzed in the kinematical and dynamical approximations of the diffraction theory. Simulations have been performed for the L{sub 3} absorption edge of yttrium in a single-crystal YFe{sub 2} film; they have shown that the magneto-optical constants (or, equivalently, the dispersion corrections to the atomic scattering factor) for hard X-rays can be determined from this dependence. Comparison with the experimental data obtained for a Nb(4 nm)/YFe{sub 2}(40 nm〈110〉)/Fe(1.5 nm)/Nb(50 nm)/sapphire sample at the European Synchrotron Radiation Facility has been made.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Modification of Graphene on a Copper Grid during Femtosecond Laser Irradiation: Electron Diffraction and Raman Spectroscopy Studies

The modification of a graphene sheet, which was fabricated by chemical vapor deposition on a close-meshed copper grid, during powerful femtosecond laser irradiation is studied. The process of long-term irradiation of a sample in vacuum is found to be accompanied by (1) breaking carbon bonds, which is indicated by a decrease in the intensities of the reflections corresponding to electron-beam diffraction by graphene and (2) the formation of new products, which is indicated by the appearance of new diffraction rings and a change in the Raman spectrum of the sample. The compositions of the forming chemical compounds are analyzed. Copper oxides Cu{sub 2}O and CuO are shown to form predominantly on the sample surface as a result of the chemical reactions induced by powerful femtosecond laser pulses.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Neutron Spin Rotation at Laue Diffraction in a Weakly Deformed Transparent Crystal with No Center of Symmetry

The effect of neutron spin rotation at Laue diffraction in a weakly deformed neutron-transparent noncentrosymmetric crystal has been described theoretically and studied experimentally. The effect is due to the bending of a Kato trajectory of the neutron in the deformed crystal. At a certain type of deformation, one of two neutron waves excited at Laue diffraction, which propagate in opposite crystal fields in the crystal with no center of symmetry, leaves the crystal. As a result, the spin of the remaining neutron wave is rotated by a certain angle with respect to initial direction due to the interaction of the magnetic moment of a moving neutron with the crystalline electric field. This effect is absent in an undeformed perfect crystal, where only the depolarization of a beam occurs because both waves in opposite electric fields have the same amplitude. A method has been developed for controlled deforming the perfect single crystal by creating a temperature gradient in it. Thereby, a new possibility of measuring electric fields acting on a neutron in noncentrosymmetric crystals, as well as a method of controlling these fields in experiments on studying the fundamental properties of the neutron, has been implemented.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Inelastic diffraction at the LHC

The relativistic scattering was one of the scientific fields where Academician V.G. Kadyshevsky has made an important and highly cited contribution [1]. In this paper we discuss the high-energy dependencies of diffractive and non-diffractive inelastic cross-sections in view of the recent LHC data which reveal a presence of the reflective scattering mode.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Intensity Distribution of the Three-Wave Diffraction from Dislocation Epitaxial Layers in the Reciprocal Space

The three-wave X-ray diffraction in strongly disordered epitaxial layers of GaN and ZnO is experimentally investigated. The charts of the intensity distribution in the reciprocal space are plotted in coordinates q{sub θ} and q{sub ϕ} for the most intensive three-wave combination (1010)/(1011) by means of subsequent θ- and ϕ-scanning. A nontrivial shape of the θ-sections of these contours at a distance from the ϕ center of reflection is revealed; it is different for different samples. For the θ-curves at the center of reflection, we observed a common peak that may be approximated by the Voigt function with a power-low decrease in the intensity at the wings; the decrease law (from–4.5 to–5.0) is found to be considerably greater than that for the similar curves of two-wave diffraction and not depending on the dislocation density and distribution in layers. In some films we observed a coarse-block structure; in addition, it follows from the distribution in the reciprocal space that these blocks are turned with respect to each other around a normal to the surface, which allows us to suggest the existence of low-angle boundaries between them, consisting exclusively of edge dislocations.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Optical Anisotropy of Photonic Crystals of Cubic Symmetry Induced by Multiple Diffraction of Light

The optical spectra of Bragg reflection from opal-like photonic crystals under conditions of the resonant enhancement of the multiple diffraction of light have been studied experimentally and theoretically using the photonic crystal structures prepared of monodisperse polystyrene globules. It is shown that the reflection signal registered in mutually orthogonal configurations of the polarizer and analyzer is related to the intrinsic optical anisotropy of the crystals and is a specific manifestation of the multiple Bragg diffraction in three-dimensional photonic crystals.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Electron-Diffraction Study of the Structure of Epitaxial Graphene Grown by the Method of Thermal Destruction of 6H- and 4H-SiC (0001) in Vacuum

The method of reflection high-energy electron diffraction (RHEED) is used for studying the structure of graphene layers formed on the surface of the Si-face of conductive and semi-insulating 6H- and 4H-SiC(0001) substrates by thermal desorption of Si atoms in high vacuum, depending on the temperature and time of sublimating Si atoms as well as depending on the method of preprocessing the substrate surface. Diffraction patterns are recorded in the [1̄21̄0] and [11̄00] crystallographic directions of the substrates. It is found that in all experiments the formation of graphene layers occurs with a rotation of the graphene crystal lattice by 30° relative to the SiC lattice.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

On the Size Effect for Neutron Diffraction by Two-Phase Structures and Applicability of Composite Standards in Analysis of Residual Austenite in Steels

The possibility of using neutron diffraction in quantitative analysis of residual austenite in steels is investigated. According to the obtained results, some properties of neutron diffraction by two-phase structures remain size-independent, which makes it possible to use large composite standards. It is shown that this approach ensures admissible accuracy without using a priori coefficients.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

High-Energy X-Ray Diffraction Microscopy in Materials Science

High-energy diffraction microscopy (HEDM) is an implementation of three-dimensional X-ray diffraction microscopy. HEDM yields maps of internal crystal orientation fields, strain states, grain shapes and locations as well as intragranular orientation distributions, and grain boundary character. Because it is nondestructive in hard materials, notably metals and ceramics, HEDM has been used to study responses of these materials to external fields including high temperature and mechanical loading. Currently available sources and detectors lead to a spatial resolution of ~1 μm and an orientation resolution of <0.1°. With the penetration characteristic of high energies ( E ≥ 50 keV), sample cross-section dimensions of ~1 mm can be studied in materials containing elements across much of the Periodic Table. This review describes hardware and software associated with HEDM as well as examples of applications. Overall, these applications include studies of grain growth, recrystallization, texture development, orientation gradients, deformation twinning, annealing twinning, plastic deformation, and additive manufacturing. We also describe relationships to other X-ray-based methods as well as prospects for further development.

36 MATERIALS SCIENCE↗

Ultrafast Imaging of Molecules with Electron Diffraction

Photoexcited molecules convert light into chemical and mechanical energy through changes in electronic and nuclear structure that take place on femtosecond timescales. Gas phase ultrafast electron diffraction (GUED) is an ideal tool to probe the nuclear geometry evolution of the molecules and complements spectroscopic methods that are mostly sensitive to the electronic state. GUED is a passive probing tool that does not alter the molecular properties during the probing process and is sensitive to the spatial distribution of charge in the molecule, including both electrons and nuclei. Improvements in temporal resolution have enabled GUED to capture coherent nuclear motions in molecules in the excited and ground electronic states with femtosecond and subangstrom resolution. Here we present the basic theory of GUED and explain what information is encoded in the diffraction signal, review how GUED has been used to observe coherent structural dynamics in recent experiments, and discuss the advantages and limitations of the method.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Ultrafast self-gating Bragg diffraction of exploding nanocrystals in an X-ray laser

In structural determination of crystalline proteins using intense femtosecond X-ray lasers, damage processes lead to loss of structural coherence during the exposure. We use a nonthermal description for the damage dynamics to calculate the ultrafast ionization and the subsequent atomic displacement. These effects degrade the Bragg diffraction on femtosecond time scales and gate the ultrafast imaging. This process is intensity and resolution dependent. At high intensities the signal is gated by the ionization affecting low resolution information first. At lower intensities, atomic displacement dominates the loss of coherence affecting high-resolution information. We find that pulse length is not a limiting factor as long as there is a high enough X-ray flux to measure a diffracted signal.

47 OTHER INSTRUMENTATION↗

Active cooling of pulse compression diffraction gratings for high energy, high average power ultrafast lasers

Laser energy absorption and subsequent heat removal from diffraction gratings in chirped pulse compressors poses a significant challenge in high repetition rate, high peak power laser development. In order to understand the average power limitations, we have modeled the time-resolved thermo-mechanical properties of current and advanced diffraction gratings. We have also developed and demonstrated a technique of actively cooling Petawatt scale, gold compressor gratings to operate at 600W of average power - a 15x increase over the highest average power petawatt laser currently in operation. As a result, combining this technique with low absorption multilayer dielectric gratings developed in our group would enable pulse compressors for petawatt peak power lasers operating at average powers well above 40kW.

42 ENGINEERING↗