scholarly journals Analysis of oscillatory rocking curve by dynamical diffraction in protein crystals

2018 ◽  
Vol 115 (14) ◽  
pp. 3634-3639 ◽  
Author(s):  
Ryo Suzuki ◽  
Haruhiko Koizumi ◽  
Keiichi Hirano ◽  
Takashi Kumasaka ◽  
Kenichi Kojima ◽  
...  
Keyword(s):  
Glucose Isomerase ◽  
Dynamical Theory ◽  
Protein Crystals ◽  
X Ray Diffraction ◽  
High Quality ◽  
Rocking Curve ◽  
Dynamical Diffraction ◽  
High Quality Protein ◽  
Good Agreement

High-quality protein crystals meant for structural analysis by X-ray diffraction have been grown by various methods. The observation of dynamical diffraction in protein crystals is an interesting topic because dynamical diffraction generally occurs in perfect crystals such as Si crystals. However, to our knowledge, there is no report yet on protein crystals showing clear dynamical diffraction. We wonder whether the perfection of protein crystals might still be low compared with that of high-quality Si crystals. Here, we present observations of the oscillatory profile of rocking curves for protein crystals such as glucose isomerase crystals. The oscillatory profiles are in good agreement with those predicted by the dynamical theory of diffraction. We demonstrate that dynamical diffraction occurs even in protein crystals. This suggests the possibility of the use of dynamical diffraction for the determination of the structure and charge density of proteins.

scholarly journals Evaluation of crystal quality of thin protein crystals based on the dynamical theory of X-ray diffraction

IUCrJ ◽  
2020 ◽  
Vol 7 (4) ◽  
pp. 761-766
Author(s):  
Marina Abe ◽  
Ryo Suzuki ◽  
Kenichi Kojima ◽  
Masaru Tachibana
Keyword(s):  
Imaging Techniques ◽  
Glucose Isomerase ◽  
Dynamical Theory ◽  
Protein Crystals ◽  
X Ray Diffraction ◽  
Rocking Curve ◽  
Dynamical Diffraction ◽  
X Ray ◽  
Equal Thickness

Knowledge of X-ray diffraction in macromolecular crystals is important for not only structural analysis of proteins but also diffraction physics. Dynamical diffraction provides evidence of perfect crystals. Until now, clear dynamical diffraction in protein crystals has only been observed in glucose isomerase crystals. We wondered whether there were other protein crystals with high quality that exhibit dynamical diffraction. Here we report the observation of dynamical diffraction in thin ferritin crystals by rocking-curve measurement and imaging techniques such as X-ray topography. It is generally known that in the case of thin crystals it is difficult to distinguish whether dynamical diffraction occurs from only rocking-curve profiles. Therefore, our results clarified that dynamical diffraction occurs in thin protein crystals because fringe contrasts similar to Pendellösung fringes were clearly observed in the X-ray topographic images. For macromolecular crystallography, it is hard to obtain large crystals because they are difficult to crystallize. For thin crystals, dynamical diffraction can be demonstrated by analysis of the equal-thickness fringes observed by X-ray topography.

Technology of high quality protein crystals’ obtaining aboard the ISS at execution of joint Japanese–Russian experiments

2020 ◽  
pp. 5-25
Author(s):  
Koji INAKA ◽  
Saori ICHIMIZU ◽  
Izumi YOSHIZAKI ◽  
Kiyohito KIHIRA ◽  
Elena G. LAVRENKO ◽  
...  
Keyword(s):  
Drug Design ◽  
International Space Station ◽  
Space Station ◽  
Protein Crystals ◽  
Diffusion Method ◽  
X Ray Diffraction ◽  
High Quality ◽  
International Space ◽  
X Ray ◽  
High Quality Protein

A series of space experiments aboard the International Space Station (ISS) associated with high-quality Protein Crystal Growth (PCG) in microgravity conditions can be considered as a unique and one of the best examples of fruitful collaboration between Japanese and Russian scientists and engineers in space, which includes also other ISS International Partners. X-ray diffraction is still the most powerful tool to determine the protein three dimensional structure necessary for Structure based drug design (SBDD). The major purpose of the experiment is to grow high quality protein crystals in microgravity for X-ray diffraction on Earth. Within one and a half decade, Japan and Russia have established an efficient process over PCG in space to support latest developments over drug design and structural biology. One of the keys for success of the experiment lies in how precisely pre-launch preparations are made. Japanese party provides flight equipment for crystallization and ensures the required environment to support the experiment aboard of the ISS’s Kibo module, and also mainly takes part of the experiment ground support such as protein sample characterization, purification, crystallization screening, and solution optimization for microgravity experiment. Russian party is responsible for integration of the flight items equipped with proteins and precipitants on board Russian transportation space vehicles (Soyuz or Progress), for delivery them at the ISS, transfer to Kibo module, and returning the experiments’ results back on Earth aboard Soyuz manned capsule. Due to close cooperation of the parties and solid organizational structure, samples can be launched at the ISS every half a year if the ground preparation goes smoothly. The samples are crystallized using counter diffusion method at 20 degree C for 1–2.5 months. After samples return, the crystals are carefully taken out from the capillary, and frozen for X-ray diffraction at SPring8 facility in Japan. Extensive support of researchers from both countries is also a part of this process. The paper analyses details of the PCG experiment scheme, unique and reliable technology of its execution, and contains examples of the application. Key words: International Space Station, Protein crystals, Microgravity, International collaboration.

scholarly journals Comparison of the Quality of Protein Crystals Grown by CLPC Seeds Method

Crystals ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 501 ◽  
Author(s):  
Li ◽  
Yan ◽  
Liu ◽  
Wu ◽  
Liu ◽  
...  
Keyword(s):  
Diffraction Data ◽  
Protein Crystal ◽  
Protein Crystals ◽  
X Ray Diffraction ◽  
High Quality ◽  
X Ray ◽  
High Quality Protein

We present a systematic quality comparison of protein crystals obtained with and without cross-linked protein crystal (CLPC) seeds. Four proteins were used to conduct the experiments, and the results showed that crystals obtained in the presence of CLPC seeds exhibited a better morphology. In addition, the X-ray diffraction data showed that the CLPC seeds method is a powerful tool to obtain high-quality protein crystals. Therefore, we recommend the use of CLPC seeds in preparing high-quality diffracting protein crystals.

A quality comparison of protein crystals grown under containerless conditions generated by diamagnetic levitation, silicone oil and agarose gel

2013 ◽  
Vol 69 (10) ◽  
pp. 1901-1910 ◽  
Author(s):  
Hui-Ling Cao ◽  
Li-Hua Sun ◽  
Jian Li ◽  
Lin Tang ◽  
Hui-Meng Lu ◽  
...  
Keyword(s):  
Silicone Oil ◽  
Crystal Quality ◽  
Protein Crystals ◽  
Agarose Gel ◽  
Resolution Limit ◽  
X Ray Diffraction ◽  
High Quality ◽  
X Ray ◽  
Diamagnetic Levitation ◽  
High Quality Protein

High-quality crystals are key to obtaining accurate three-dimensional structures of proteins using X-ray diffraction techniques. However, obtaining such protein crystals is often a challenge. Several containerless crystallization techniques have been reported to have the ability to improve crystal quality, but it is unknown which is the most favourable way to grow high-quality protein crystals. In this paper, a quality comparison of protein crystals which were grown under three containerless conditions provided by diamagnetic levitation, silicone oil and agarose gel was conducted. A control experiment on a vessel wall was also simultaneously carried out. Seven different proteins were crystallized under the four conditions, and the crystal quality was assessed in terms of the resolution limit, the mosaicity and theRmerge. It was found that the crystals grown under the three containerless conditions demonstrated better morphology than those of the control. X-ray diffraction data indicated that the quality of the crystals grown under the three containerless conditions was better than that of the control. Of the three containerless crystallization techniques, the diamagnetic levitation technique exhibited the best performance in enhancing crystal quality. This paper is to our knowledge the first report of improvement of crystal quality using a diamagnetic levitation technique. Crystals obtained from agarose gel demonstrated the second best improvement in crystal quality. The study indicated that the diamagnetic levitation technique is indeed a favourable method for growing high-quality protein crystals, and its utilization is thus potentially useful in practical efforts to obtain well diffracting protein crystals.

scholarly journals Extending the pool of compatible peptide hydrogels for protein crystallization

Crystals ◽  
2019 ◽  
Vol 9 (5) ◽  
pp. 244
Author(s):  
Guillermo Escolano-Casado ◽  
Rafael Contreras-Montoya ◽  
Mayte Conejero-Muriel ◽  
Albert Castellví ◽  
Judith Juanhuix ◽  
...  
Keyword(s):  
Protein Crystallization ◽  
Glucose Isomerase ◽  
Protein Crystals ◽  
High Quality ◽  
Short Peptide ◽  
High Quality Protein ◽  
Functional Biomaterials ◽  
Peptide Hydrogels

Short-peptide supramolecular (SPS) hydrogels are a class of materials that have been found to be useful for (bio)technological applications thanks to their biocompatible nature. Among the advantages reported for these peptides, their economic affordability and easy functionalization or modulation have turned them into excellent candidates for the development of functional biomaterials. We have recently demonstrated that SPS hydrogels can be used to produce high-quality protein crystals, improve their properties, or incorporate relevant materials within the crystals. In this work, we prove that hydrogels based on methionine and tyrosine are also good candidates for growing high-quality crystals of the three model proteins: lysozyme, glucose isomerase, and thaumatin.

scholarly journals Влияние толщины пленки Pt на изменение текстуры и доли кристаллической фазы при ее отжиге

2020 ◽  
Vol 90 (5) ◽  
pp. 795
Author(s):  
Р.В. Селюков ◽  
В.В. Наумов
Keyword(s):  
Volume Fraction ◽  
Curve Analysis ◽  
X Ray Diffraction ◽  
Rocking Curve ◽  
X Ray ◽  
Texture Parameters ◽  
Sputter Deposited ◽  
Pt Films ◽  
H 20

Textured Pt films with thickness h=20-80 nm were sputter deposited on oxidized c-Si (100) wafers and annealed in vacuum at 500°C/60 min. The thickness dependencies of the crystalline texture parameters and of the fraction of crystalline phase δ are obtained for as-deposited and annealed films using X-ray diffraction. The determination of δ in textured films is carried out by the new method based on rocking curve analysis. It is found that annealing leads to the texture improvement and to the increasing of δ for all h. The less h, the stronger effects of texture improvement and of δ increasing. These results are explained by the annealing-induced formation of large secondary grains whose volume fraction increases as h decreases. The inhomogeneity of the depth distributions of texture parameters and of δ are investigated for the as-deposited Pt films.

scholarly journals Experimentally obtained and computer-simulated X-ray non-coplanar 18-beam pinhole topographs for a silicon crystal

2019 ◽  
Vol 75 (3) ◽  
pp. 483-488 ◽  
Author(s):  
Kouhei Okitsu ◽  
Yasuhiko Imai ◽  
Yoshitaka Yoda
Keyword(s):  
Silicon Crystal ◽  
Dynamical Theory ◽  
X Rays ◽  
X Ray Diffraction ◽  
X Ray ◽  
Good Agreement

Non-coplanar 18-beam X-ray pinhole topographs for a silicon crystal were computer simulated by fast Fourier transforming the X-ray rocking amplitudes that were obtained by solving the n-beam (n = 18) Ewald–Laue dynamical theory (E-L&FFT method). They were in good agreement with the experimentally obtained images captured using synchrotron X-rays. From this result and further consideration based on it, it has been clarified that the X-ray diffraction intensities when n X-ray waves are simultaneously strong in the crystal can be computed for any n by using the E-L&FFT method.

Effect of C and Ge Concentration On The Thermal Stability of RTCVD Grown Si1-x-yGexCy Alloys

1997 ◽  
Vol 470 ◽  
Author(s):  
Patricia Warren ◽  
Stephane Retzmanick ◽  
Martin Gotza ◽  
Marc Begems
Keyword(s):  
Lattice Constant ◽  
Strain Relaxation ◽  
Mechanical Strain ◽  
Chemical Vapor ◽  
Misfit Dislocations ◽  
X Ray Diffraction ◽  
Cubic Silicon Carbide ◽  
Kinetics Of ◽  
Good Agreement

ABSTRACTSi / Si1-x-yGexCy / Si heterostructures containing up to 17 at.% Ge and 1.9 at.% C were grown on (001) silicon by low pressure Rapid Thermal Chemical Vapor Deposition, using a mixture of silane, germane and methylsilane, diluted in hydrogen. The samples were then annealed in a Rapid Thermal Processing furnace, under an atmospheric pressure of nitrogen, at temperatures ranging from 900 to 1130 °C.The samples were characterized using infrared spectroscopy and x-ray diffraction. SIMS profiling and TEM observation were performed on some of the samples.Substitutional C gradually disappeared, either precipitating out to form cubic silicon carbide (β-SiC), or simply vanishing into interstitial positions. In any case, the in-plane lattice constant remained constant after annealing, indicating that there was no mechanical strain relaxation by formation of misfit dislocations. The perpendicular lattice constant increased due to the decrease in substitutional C concentration, as well as it decreased due to the germanium out-diffusion. This variation of the strain during annealing was modeled, and allowed the determination of the kinetics of the substitutional carbon disappearance. The same behavior was observed for all samples. Indeed, the Cs disappearance rate was always increased for samples with higher initial Ge and C concentrations. The kinetics of this precipitation was found in very good agreement with previous published results.

TEM Study of the Morphology Of GaN/SiC (0001) Grown at Various Temperatures by MBE

1999 ◽  
Vol 595 ◽  
Author(s):  
W.L. Sarney ◽  
L. Salamanca-Riba ◽  
V. Ramachandran ◽  
R.M Feenstra ◽  
D.W. Greve
Keyword(s):  
Low Temperatures ◽  
Stacking Faults ◽  
Full Width ◽  
X Ray Diffraction ◽  
High Quality ◽  
Double Crystal ◽  
Tem Analysis ◽  
Rocking Curve ◽  
X Ray ◽  
Substrate Temperatures

AbstractGaN films grown on SiC (0001) by MBE at various substrate temperatures (600° - 750° C) were characterized by RHEED, STM, x-ray diffraction, AFM and TEM. This work focuses on the TEM analysis of the films' features, such as stacking faults and dislocations, which are related to the substrate temperature. There are several basal plane stacking faults in the form of cubic inclusions for samples grown at low temperatures compared to those grown at high temperatures. The dislocation density is greatest for the film grown at 600°C, and it steadily decreases with increasing growth temperatures. Despite the presence of various defects, x-ray analysis shows that the GaN films are of high quality. The double crystal rocking curve full width at half maximum (FWHM) for the GaN (0002) peak is less than 2 arc-minutes for all of the films we measured and it decreases with increasing growth temperature.

Enhancement of nucleation of protein crystals on nano-wrinkled surfaces

2016 ◽  
Vol 186 ◽  
pp. 187-197 ◽  
Author(s):  
Praveen K. Bommineni ◽  
Sudeep N. Punnathanam
Keyword(s):  
Free Energy ◽  
Protein Concentration ◽  
Protein Crystallization ◽  
Crystal Nucleation ◽  
Protein Crystal ◽  
Protein Crystals ◽  
Free Energy Barrier ◽  
High Quality ◽  
High Quality Protein ◽  
Sinusoidal Surface

The synthesis of high quality protein crystals is essential for determining their structure. Hence the development of strategies to facilitate the nucleation of protein crystals is of prime importance. Recently, Ghatak and Ghatak [Langmuir 2013, 29, 4373] reported heterogeneous nucleation of protein crystals on nano-wrinkled surfaces. Through a series of experiments on different proteins, they were able to obtain high quality protein crystals even at low protein concentrations and sometimes without the addition of a precipitant. In this study, the mechanism of protein crystal nucleation on nano-wrinkled surfaces is studied through Monte Carlo simulations. The wrinkled surface is modeled by a sinusoidal surface. Free-energy barriers for heterogeneous crystal nucleation on flat and wrinkled surfaces are computed and compared. The study reveals that the enhancement of nucleation is closely related to the two step nucleation process seen during protein crystallization. There is an enhancement of protein concentration near the trough of the sinusoidal surface which aids in nucleation. However, the high curvature at the trough acts as a deterrent to crystal nucleus formation. Hence, significant lowering of the free-energy barrier is seen only if the increase in the protein concentration at the trough is very high.

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