Large-Scale Domain Movements and Hydration Structure Changes in the Active-Site Cleft of Unligated Glutamate Dehydrogenase fromThermococcus profundusStudied by Cryogenic X-ray Crystal Structure Analysis and Small-Angle X-ray Scattering†,‡

Biochemistry ◽  
2001 ◽  
Vol 40 (10) ◽  
pp. 3069-3079 ◽  
Author(s):  
Masayoshi Nakasako ◽  
Testuro Fujisawa ◽  
Shin-ichi Adachi ◽  
Toshiaki Kudo ◽  
Sadaharu Higuchi
Keyword(s):  
Crystal Structure ◽  
Glutamate Dehydrogenase ◽  
Small Angle ◽  
Active Site ◽  
Large Scale ◽  
Crystal Structure Analysis ◽  
X Ray ◽  
X Ray Scattering ◽  
Structure Changes ◽  
Active Site Cleft

Structural refinement by restrained molecular-dynamics algorithm with small-angle X-ray scattering constraints for a biomolecule

2004 ◽  
Vol 37 (1) ◽  
pp. 103-109 ◽  
Author(s):  
Masaki Kojima ◽  
Alexander A. Timchenko ◽  
Junichi Higo ◽  
Kazuki Ito ◽  
Hiroshi Kihara ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Small Angle ◽  
Protein Structures ◽  
Saxs Data ◽  
X Ray ◽  
X Ray Scattering ◽  
Saxs Curve ◽  
Restrained Molecular Dynamics ◽  
Ray Scattering

A new algorithm to refine protein structures in solution from small-angle X-ray scattering (SAXS) data was developed based on restrained molecular dynamics (MD). In the method, the sum of squared differences between calculated and observed SAXS intensities was used as a constraint energy function, and the calculation was started from given atomic coordinates, such as those of the crystal. In order to reduce the contribution of the hydration effect to the deviation from the experimental (objective) curve during the dynamics, and purely as an estimate of the efficiency of the algorithm, the calculation was first performed assuming the SAXS curve corresponding to the crystal structure as the objective curve. Next, the calculation was carried out with `real' experimental data, which yielded a structure that satisfied the experimental SAXS curve well. The SAXS data for ribonuclease T1, a single-chain globular protein, were used for the calculation, along with its crystal structure. The results showed that the present algorithm was very effective in the refinement and adjustment of the initial structure so that it could satisfy the objective SAXS data.

The nature of the scattering tail in Cu–Ni–Fe and Invar alloys investigated by anomalous small-angle X-ray scattering

1991 ◽  
Vol 24 (6) ◽  
pp. 1027-1034 ◽  
Author(s):  
J. P. Simon ◽  
O. Lyon
Keyword(s):  
Small Angle ◽  
Large Scale ◽  
Concentration Fluctuations ◽  
X Ray ◽  
Invar Alloys ◽  
X Ray Scattering ◽  
Angle Measurements ◽  
Two Systems ◽  
Fe Alloys ◽  
Ray Scattering

A large rapidly decreasing intensity called the `scattering tail' is generally observed at the smallest recorded angles during small-angle measurements of metallic alloys. Since this tail was interpreted as caused by a bimodal phase separation in Cu–Ni–Fe alloys and by long-wavelength concentration fluctuations in Invar alloys, these two systems were re-examined with anomalous X-ray scattering. The variation of the alloying atomic contrasts allows a discrimination between the different types of particles or defects. In neither of the two systems can the tails be interpreted as caused by large-scale concentration fluctuations. In Cu–Ni–Fe alloys, the tail is due to some kind of superficial defect (surface roughness etc.). In Invar alloys, the tail is probably due to residual impurity particles.

Crystal Structure Analysis in the Dehydrogenation Process of Mg(NH2)2-LiH System

2006 ◽  
Vol 971 ◽  
Author(s):  
Tatsuo Noritake ◽  
Masakazu Aoki ◽  
Shin-ichi Towata ◽  
Yuko Nakamori ◽  
Shin-ichi Orimo
Keyword(s):  
Crystal Structure ◽  
Rietveld Analysis ◽  
Crystal Structure Analysis ◽  
Diffraction Measurement ◽  
Hydrogen Storage Materials ◽  
X Ray Diffraction ◽  
X Ray ◽  
Structure Changes ◽  
Li Ion ◽  
Cation Sites

ABSTRACTMg(NH2)2-LiH system which have the properties of reversible hydrogenation and dehydrogenation is one of the promising candidates for new hydrogen storage materials. For understanding of the reversible reaction mechanism, we investigated the crystal structure changes in 3Mg(NH2)2-12LiH system using the pressure-composition (p-c) isotherm measurement and synchrotron X-ray diffraction. The sample was prepared by the hydrogenation of Mg3N2 + 4Li3N. At the several dehydrogenation stages of the p-c isotherm measurement at temperature 523 K, the sample was taken out and X-ray diffraction measurement was performed. By the amount of desorbed hydrogen, the reaction was expressed as the following formula, Mg(NH2)2 + 4LiH → LixMg(NH2)2-x(NH)x + (4-x)LiH + xH2 (x = 0∼2). The crystal structures of LixMg(NH2)2-x(NH)x, similar to CaF2-type one, formed during the dehydrogenation reaction were determined by Rietveld analysis. As a result, it is considered that the dehydrogenation process might relate to the diffusion of Li+ ion in cation sites of Mg(NH2)2.

Small-angle X-ray scattering by PVP–water mixtures

2001 ◽  
Vol 34 (1) ◽  
pp. 62-64 ◽  
Author(s):  
Jan van der Elsken ◽  
Wim Bras ◽  
Jan Michielsen
Keyword(s):  
Small Angle ◽  
Large Scale ◽  
Columnar Structure ◽  
Water Mixture ◽  
X Ray ◽  
Large Scale Structures ◽  
X Ray Scattering ◽  
Angle Scattering ◽  
Hexagonal Columnar ◽  
Ray Scattering

Small-angle X-ray scattering experiments reveal the formation of large-scale structures when a 60 wt% poly(vinylpyrrolidone) (PVP)–water mixture is cooled to 260 K. The formation of these structures leads to an enhancement of continuous small-angle scattering with decreasing temperature. This is accompanied by the appearance of sharp Bragg peaks that have a very short lifetime. The scattering angles of these peaks are in accordance with a hexagonal columnar structure. It appears that such structures occasionally live long enough to undergo rotational Brownian motion.

Practical Synthesis of a PCP-Type Pincer Ligand and Its Metal Complexes­

Synthesis ◽  
2017 ◽  
Vol 50 (05) ◽  
pp. 1015-1019 ◽  
Author(s):  
Kazutaka Matoba ◽  
Yoshiaki Nishibayashi ◽  
Aya Eizawa ◽  
Shunsuke Nishimura ◽  
Kazuya Arashiba ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Transition Metal ◽  
Metal Complexes ◽  
Transition Metal Complexes ◽  
Large Scale ◽  
Crystal Structure Analysis ◽  
Synthetic Method ◽  
Pincer Ligand ◽  
X Ray ◽  
Practical Synthesis

A synthetic method for N-heterocyclic carbene- and phosphine-based PCP-type pincer ligand is described on a large scale. Some transition-metal complexes bearing the PCP-type pincer ligand are prepared and characterized by X-ray crystal structure analysis.

Sign in / Sign up

Export Citation Format

Share Document