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.

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.

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.

Recrystallization: a method to improve the quality of protein crystals

2015 ◽  
Vol 48 (3) ◽  
pp. 758-762 ◽  
Author(s):  
Hai Hou ◽  
Yue Liu ◽  
Bo Wang ◽  
Fan Jiang ◽  
Hao-Ran Tao ◽  
...  
Keyword(s):  
Crystal Quality ◽  
Proteinase K ◽  
Protein Crystals ◽  
Structural Determination ◽  
X Ray Diffraction ◽  
X Ray ◽  
X Ray Crystallography ◽  
High Quality Protein ◽  
Before And After

The quality of protein crystals is an important parameter for structural determination with X-ray crystallography. Indeed, a prerequisite for obtaining high-resolution diffraction data is that the crystals be of sufficient quality. However, obtaining high-quality protein crystals is a well known bottleneck to protein structural determination that remains a difficult task. In this paper, it is demonstrated that recrystallization can be an effective method of improving the quality of protein crystals. Five proteins, lysozyme, proteinase K, concanavalin A, thaumatin and catalase, were used for this investigation, and the crystal quality of these proteins was examined using X-ray diffraction before and after recrystallization. Comparisons of the crystals before and after recrystallization verified that recrystallization not only enhanced the morphology of the crystals but also improved crystal quality. Therefore, it is proposed that recrystallization might be a useful alternative method for obtaining protein crystals with enhanced diffraction.

scholarly journals Crystallographic features of ammonium fluoroelpasolites: dynamic orientational disorder in crystals of (NH4)3HfF7 and (NH4)3Ti(O2)F5

2017 ◽  
Vol 73 (1) ◽  
pp. 1-9 ◽  
Author(s):  
Anatoly A. Udovenko ◽  
Alexander A. Karabtsov ◽  
Natalia M. Laptash
Keyword(s):  
Single Crystal ◽  
Electron Density ◽  
Diffraction Data ◽  
Central Atom ◽  
X Ray Diffraction ◽  
Dynamic Nature ◽  
Orientational Disorder ◽  
High Quality ◽  
Structural Units ◽  
X Ray

A classical elpasolite-type structure is considered with respect to dynamically disordered ammonium fluoro-(oxofluoro-)metallates. Single-crystal X-ray diffraction data from high quality (NH4)3HfF7 and (NH4)3Ti(O2)F5 samples enabled the refinement of the ligand and cationic positions in the cubic Fm \bar 3 m (Z = 4) structure. Electron-density atomic profiles show that the ligand atoms are distributed in a mixed (split) position instead of 24e. One of the ammonium groups is disordered near 8c so that its central atom (N1) forms a tetrahedron with vertexes in 32f. However, a center of another group (N2) remains in the 4b site, whereas its H atoms (H2) occupy the 96k positions instead of 24e and, together with the H3 atom in the 32f position, they form eight spatial orientations of the ammonium group. It is a common feature of all ammonium fluoroelpasolites with orientational disorder of structural units of a dynamic nature.

scholarly journals Redetermination of Sr2PdO3 from single-crystal X-ray data

2019 ◽  
Vol 75 (1) ◽  
pp. 30-32
Author(s):  
Gohil S. Thakur ◽  
Hans Reuter ◽  
Claudia Felser ◽  
Martin Jansen
Keyword(s):  
Crystal Structure ◽  
Single Crystal ◽  
Diffraction Data ◽  
Structure Refinement ◽  
Structure Type ◽  
X Ray Diffraction ◽  
High Quality ◽  
X Ray ◽  
Cell Parameters ◽  
Anisotropic Displacement Parameters

The crystal structure redetermination of Sr2PdO3 (distrontium palladium trioxide) was carried out using high-quality single-crystal X-ray data. The Sr2PdO3 structure has been described previously in at least three reports [Wasel-Nielen & Hoppe (1970). Z. Anorg. Allg. Chem. 375, 209–213; Muller & Roy (1971). Adv. Chem. Ser. 98, 28–38; Nagata et al. (2002). J. Alloys Compd. 346, 50–56], all based on powder X-ray diffraction data. The current structure refinement of Sr2PdO3, as compared to previous powder data refinements, leads to more precise cell parameters and fractional coordinates, together with anisotropic displacement parameters for all sites. The compound is confirmed to have the orthorhombic Sr2CuO3 structure type (space group Immm) as reported previously. The structure consists of infinite chains of corner-sharing PdO4 plaquettes interspersed by SrII atoms. A brief comparison of Sr2PdO3 with the related K2NiF4 structure type is given.

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.

The X-Ray Powder Diffraction Patterns and Crystal Structure for Al2M3Y(M=Cu, Ni)

2014 ◽  
Vol 950 ◽  
pp. 48-52
Author(s):  
De Gui Li ◽  
Ming Qin ◽  
Liu Qing Liang ◽  
Zhao Lu ◽  
Shu Hui Liu ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Hexagonal Structure ◽  
Argon Atmosphere ◽  
X Ray Diffraction ◽  
High Quality ◽  
X Ray ◽  
Arc Melting ◽  
Diffraction Patterns

The Al2M3Y(M=Cu, Ni) compound was synthesized by arc melting under argon atmosphere. The high-quality powder X-ray diffraction data of Al2M3Y have been presented. The refinement of the X-ray diffraction patterns for the Al2M3Y compound show that the Al2M3Y has hexagonal structure, space groupP6/mmm(No.191), with a = b = 5.1618(2) Å, c = 4.1434(1) Å,V= 95.6 Å3,Z= 1,ڑx= 5.7922 g/cm3,F30= 155.5(0.0057, 34), RIR = 2.31 for Al2Cu3Y, and with a = b = 5.0399(1) Å, c = 4.0726(1) Å,V= 89.59 Å3,Z= 1,ڑx= 5.9118 g/cm3,F30= 135.7(0.0072, 30), RIR = 2.54 for Al2Ni3Y.

Crystallization of high-quality protein crystals using an external electric field

2015 ◽  
Vol 48 (5) ◽  
pp. 1507-1513 ◽  
Author(s):  
H. Koizumi ◽  
S. Uda ◽  
K. Fujiwara ◽  
M. Tachibana ◽  
K. Kojima ◽  
...  
Keyword(s):  
Electric Field ◽  
External Electric Field ◽  
Applied Field ◽  
Local Strain ◽  
Protein Crystal ◽  
X Ray Diffraction ◽  
High Quality Protein ◽  
Hen Egg White ◽  
Lysozyme Crystals

The effect of a 20 kHz external electric field on the quality of tetragonal hen egg white (HEW) lysozyme crystals was investigated using X-ray diffraction rocking-curve measurements. The full width at half-maximum was found to be larger for high-order reflections but smaller for low-order reflections. In particular, it was revealed that a large amount of local strain is accumulated in tetragonal HEW lysozyme crystals grown under an applied field at 20 kHz. Comparison with previous results obtained for crystals grown with an applied field at 1 MHz [Koizumi, Uda, Fujiwara, Tachibana, Kojima & Nozawa (2013).J. Appl. Cryst.46, 25–29] indicated that improvement of the protein crystal quality could be achieved by selection of an appropriate frequency for the applied electric field, which has a significant effect on the growth of the solid.

Numerical Analysis of the Diffusive Field around a Growing Protein Crystal in Microgravity

2012 ◽  
Vol 323-325 ◽  
pp. 565-569 ◽  
Author(s):  
Koji Inaka ◽  
Hiroaki Tanaka ◽  
Sachiko Takahashi ◽  
Satoshi Sano ◽  
Masaru Sato ◽  
...  
Keyword(s):  
Numerical Analysis ◽  
Kinetic Constant ◽  
Protein Crystal ◽  
Microgravity Environment ◽  
X Ray Diffraction ◽  
X Ray ◽  
Microgravity Experiments ◽  
Space Agency ◽  
Filtration Effect

t is believed that a microgravity environment may maintain ideal depletion zones of protein (PDZ) and impurity (IDZ) around growing crystals and may contribute to growing high-quality crystals. This can lead to an X-ray diffraction data collection of higher resolution with lower mosaicity, because of the better internal order and fewer defects in the crystals when compared to ground-grown crystals. The extent of these depletion zones are dependent on a competition between the diffusion of the molecules in the solution (indexed by the diffusion coefficient, D) and the adsorption of those into the growing crystal (indexed by the kinetic constant, β). If we use the D/β value as an index of the extent of PDZ and IDZ, a lower D/β value is ideal for maintaining PDZ and IDZ. Using experimental results, we could easily obtain the D/β value. When we combined the D/β value with the quality of protein crystals obtained in microgravity experiments provided by Japanese Space Agency (JAXA), we found that the effects of microgravity contributed to obtaining superior crystals especially if the D/β value was less than 3 mm. The numerical analysis of the PDZ and IDZ shows that the radius of the crystal (R) is also related to the PDZ and the IDZ. If the Rβ/D value is large, both the PDZ and the IDZ provide a filtration effect, but if the Rβ/D value is small, only the IDZ does.

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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