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.

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.

scholarly journals X-ray transparent microfluidic platforms for membrane protein crystallization with microseeds

Lab on a Chip ◽  
2018 ◽  
Vol 18 (6) ◽  
pp. 944-954 ◽  
Author(s):  
Jeremy M. Schieferstein ◽  
Ashtamurthy S. Pawate ◽  
Michael J. Varel ◽  
Sudipto Guha ◽  
Ieva Astrauskaite ◽  
...  
Keyword(s):  
Membrane Protein ◽  
Protein Crystallization ◽  
Protein Crystals ◽  
Microfluidic Platforms ◽  
High Quality ◽  
X Ray ◽  
High Quality Protein ◽  
Membrane Protein Crystallization

Microfluidic platforms for formulation of crystallization trials with microseeds to enable the growth of high-quality protein crystals.

Crystallization Technique of High-Quality Protein Crystals Controlling Surface Free Energy

2017 ◽  
Vol 17 (12) ◽  
pp. 6712-6718 ◽  
Author(s):  
Haruhiko Koizumi ◽  
Satoshi Uda ◽  
Katsuo Tsukamoto ◽  
Masaru Tachibana ◽  
Kenichi Kojima ◽  
...  
Keyword(s):  
Free Energy ◽  
Surface Free Energy ◽  
Protein Crystals ◽  
High Quality ◽  
High Quality Protein

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.

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 High quality protein crystal growth under microgravity in JAXA PCG project

2011 ◽  
Vol 67 (a1) ◽  
pp. C460-C460
Author(s):  
M. Sato ◽  
H. Tanaka ◽  
K. Inaka ◽  
S. Sano ◽  
M. Masaki ◽  
...  
Keyword(s):  
Crystal Growth ◽  
Protein Crystal ◽  
High Quality ◽  
High Quality Protein ◽  
Protein Crystal Growth

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.

Nucleation of protein crystals – a nanoscopic perspective

Nanoscale ◽  
2018 ◽  
Vol 10 (26) ◽  
pp. 12256-12267 ◽  
Author(s):  
Mike Sleutel ◽  
Alexander E. S. Van Driessche
Keyword(s):  
State Of The Art ◽  
Crystal Nucleation ◽  
Protein Crystal ◽  
Protein Crystals ◽  
Historical Overview ◽  
Art Analysis

A historical overview and state-of-the-art analysis of the mechanism of protein crystal nucleation from an experimentalist's perspective.

scholarly journals Microscope detection options for colorless protein crystals grown in lipidic cubic phases

2003 ◽  
Vol 36 (5) ◽  
pp. 1295-1296 ◽  
Author(s):  
Peter Nollert
Keyword(s):  
Membrane Proteins ◽  
Crystal Nucleation ◽  
Protein Crystal ◽  
Protein Crystals ◽  
Cubic Phase ◽  
Polarization Microscopy ◽  
Cubic Phases ◽  
Lipidic Cubic Phase ◽  
Surface Distortions ◽  
Microscopic Techniques

The use of lipidic cubic phases as crystal nucleation and growth matrices is becoming popular and has yielded crystals of soluble and membrane proteins. So far, all of the membrane proteins crystallized by this method have been colored. This feature has facilitated the detection of the often encountered microcrystals in initial screening rounds. Indeed, small colorless protein crystals have poor optical contrast as a result of the small differences in refractive index of the protein crystal and the surrounding lipidic cubic phase. While a perfect preparation of a lipidic cubic phase is transparent and optically isotropic, in a crystallization setup it frequently disguises crystals due to cracks, inclusions, surface distortions and phase boundaries. Here, several specialized microscopic techniques and illumination conditions are compared and it is found that sufficient contrast is generated by cross polarization microscopy and by Hoffman modulation contrast microscopy for the detection of colorless protein crystals.

Pressure-induced high-density amorphous ice in protein crystals

2008 ◽  
Vol 41 (1) ◽  
pp. 1-7 ◽  
Author(s):  
Chae Un Kim ◽  
Yi-Fan Chen ◽  
Mark W. Tate ◽  
Sol M. Gruner
Keyword(s):  
High Pressure ◽  
Ambient Pressure ◽  
Protein Crystallization ◽  
High Density ◽  
Protein Crystal ◽  
Protein Crystals ◽  
X Ray ◽  
Crystallization Solution ◽  
Highly Correlated

Crystal cryocooling has been used in X-ray protein crystallography to mitigate radiation damage during diffraction data collection. However, cryocooling typically increases crystal mosaicity and often requires a time-consuming search for cryoprotectants. A recently developed high-pressure cryocooling method reduces crystal damage relative to traditional cryocooling procedures and eases or eliminates the need to screen for cryoprotectants. It has been proposed that the formation of high-density amorphous (HDA) ice within the protein crystal is responsible for the excellent diffraction quality of the high-pressure cryocooled crystals. This paper reports X-ray data that confirm the presence of HDA ice in the high-pressure cryocooled protein crystallization solution and protein crystals analyzed at ambient pressure. Diffuse scattering with a spacing characteristic of HDA ice is seen at low temperatures. This scattering then becomes characteristic successively to low-density amorphous, cubic and hexagonal ice phases as the temperature is gradually raised from 80 to 230 K, and seems to be highly correlated with the diffraction quality of crystals.

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