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PubMed2004

Role of curvature elasticity in sectorization and ripple formation during melt crystallization of polymer single crystals.

The present article focuses on theoretical elucidation of possible effect of mechanical deformation on spatio-temporal emergence of unusual polymer morphology subjected to quiescent isothermal crystallization conditions. The present theory developed is based on a phase field model consisted of non-conserved time dependent Ginzburg-Landau equation having an asymmetric double well potential in the crystal order parameter signifying metastability for crystallization, coupled with the chain tilt angle involving curvature elasticity and strain recovery potentials. Under quiescent crystallization conditions, the curvature elasticity term is needed to discern the emergence of sectorized single crystals. Upon coupling with the strain recovery potential, the numerical calculation captures ripple formation running across the long lamellar growth front, which may be attributed to lamellar buckling caused by the volume shrinkage. Of particular interest is that these simulated topologies of the single crystals are in good accord with the growth character of syndiotactic polypropylene single crystals observed experimentally by us during isothermal crystallization from the melt.

Journal Article↗
PubMed2005

Crystallization and crystal manipulation of the Pterocarpus angolensis seed lectin.

The Man/Glc-specific legume lectin from the seeds of the African bloodwood tree (Pterocarpus angolensis) was crystallized in the presence of the disaccharide ligand Man(alpha1-3)ManMe. Small crystals initially appeared from a preliminary screen, but proved difficult to reproduce. The initial crystals were used to prepare microseeds, leading to a reproducible crystallization protocol. All attempts to obtain crystals directly of the ligand-free protein or of other carbohydrate complexes failed. However, the Man(alpha1-3)ManMe co-crystals withstand soaking with ten other carbohydrates known to bind to the lectin. Soaking for 15 min in 100 mM carbohydrate typically resulted in complete replacement of Man(alpha1-3)ManMe by the desired carbohydrate despite the involvement of lattice contacts at the binding site. Transferring the crystals for two weeks in carbohydrate-free artificial mother liquor resulted in the complete removal of the sugar from one of the two monomers in the asymmetric unit. Additional treatment of these crystals with 100 mM EDTA for two weeks resulted in removal of the structural calcium and manganese ions, which is accompanied by significant structural rearrangements of the loops that constitute the carbohydrate-binding site.

Crystallography, X-Ray↗
PubMed1995

Backscattered electron imaging of crystal matrix protein on the surface of calcium oxalate crystals using colloidal gold.

In order to clarify the presence and localization of crystal matrix protein (CMP) upon calcium oxalate crystals, scanning electron microscopy (SEM) and backscattered electron imaging (BEI) techniques were used. This protein exhibits a remarkable affinity with calcium oxalate crystals and may be important in stone pathogenesis. In this paper, rabbit anti-human CMP polyclonal antibody was used as first antibody, and for the second antibody, goat anti-rabbit IgG conjugated with 20 nm immunogold was used. Freshly prepared crystals from male urine were fixed in SEM fixative, then blocked and washed with phosphate-buffered saline and bovine serum albumin (PBS/BSA). First and second antibodies were reacted in PBS/BSA. Crystals were then dehydrated and finally coated for SEM study. The SEM technique showed bipyramidal shaped dihydrate calcium oxalate crystals in every sample and even at high magnification, colloidal gold could barely be seen. BEI clearly demonstrated the presence and localization of the gold on the surface of the crystals as well as on the macromolecules eluted from the crystals by dissolving them in ethylenediamminetetraacetic acid solution.

Calcium Oxalate↗
PubMed1993

Observations on structural features and characteristics of biological apatite crystals. 6. Observation on lattice imperfection of human tooth and bone crystals. I.

In a series of studies to investigate the basic structural features and characteristics of the biological apatite crystals, using an electron microscope, we examined the ultrastructure of the human enamel, dentin, and bone crystals at near atomic resolution and showed the configuration of the hydroxyapatite structure through the cross and longitudinal sections of the crystals. Subsequently, based on the results of the observations by the authors of the ultrastructure of the tooth and bone, using the same approach, we have been able to directly examine the images of the lattice imperfections in the human enamel, dentin, and bone crystals, such as the point defect structures and dislocations in the crystals. In this report, we describe the image of the point defect structures and line defect structures obtained, using the same approach from the sections of the human enamel, dentin, and bone crystals. The materials used for this study were the noncarious enamel and dentin from the freshly extracted human erupted lower first molars, and bone tissue obtained from the alveolar compact bone. The small cubes of the material were fixed in glutaraldehyde and osmium tetroxide and embedded in epoxy resin using the routine methods. The ultrathin sections were cut with a diamond knife without decalcification. The sections were examined with the HITACHI H-800 H and H-9000 types of transmission electron microscopes operated at 200 kV and 300 kV. Each crystal was observed at the initial magnification of 300,000-500,000 times and at the final magnification of 10,000,000 times and over. We sincerely believe that the electron micrographs shown in this report are the first to show the images of the lattice imperfections in the human enamel, dentin, and bone crystals, such as the point defect and line defect structures, at near atomic resolution.

Alveolar Process↗
PubMed2001

Crystal structure of the 30 S ribosomal subunit from Thermus thermophilus: purification, crystallization and structure determination.

We describe the crystallization and structure determination of the 30 S ribosomal subunit from Thermus thermophilus. Previous reports of crystals that diffracted to 10 A resolution were used as a starting point to improve the quality of the diffraction. Eventually, ideas such as the addition of substrates or factors to eliminate conformational heterogeneity proved less important than attention to detail in yielding crystals that diffracted beyond 3 A resolution. Despite improvements in technology and methodology in the last decade, the structure determination of the 30 S subunit presented some very challenging technical problems because of the size of the asymmetric unit, crystal variability and sensitivity to radiation damage. Some steps that were useful for determination of the atomic structure were: the use of anomalous scattering from the LIII edges of osmium and lutetium to obtain the necessary phasing signal; the use of tunable, third-generation synchrotron sources to obtain data of reasonable quality at high resolution; collection of derivative data precisely about a mirror plane to preserve small anomalous differences between Bijvoet mates despite extensive radiation damage and multi-crystal scaling; the pre-screening of crystals to ensure quality, isomorphism and the efficient use of scarce third-generation synchrotron time; pre-incubation of crystals in cobalt hexaammine to ensure isomorphism with other derivatives; and finally, the placement of proteins whose structures had been previously solved in isolation, in conjunction with biochemical data on protein-RNA interactions, to map out the architecture of the 30 S subunit prior to the construction of a detailed atomic-resolution model.

Crystallization↗
PubMed2000

Crystallization of the F41 fragment of flagellin and data collection from extremely thin crystals.

Flagellin, which constructs supercoiled filaments of the bacterial flagellum, is very difficult to crystallize because of its strong tendency to polymerize. We therefore crystallized the F41 fragment of flagellin, which does not polymerize because terminal regions that play important roles in polymerization are cleaved off. F41 was crystallized by the hanging drop vapor diffusion method in a mixture of polyethylene glycol, glycerol, and isopropanol, with a reservoir solution covered with silicon oil. The two key factors for success in growing sufficiently large crystals were isopropanol and silicon oil, which worked well to reduce the otherwise very high nucleation rate that resulted in hundreds of tiny crystals. The crystals were grown to very thin plates with thickness less than 10 microm, which made the collection of diffraction data very difficult. Freezing and annealing of the crystals and irradiation at synchrotron beamlines had to be carried out by specific methods and under specific conditions for its structure analysis at 2.0-A resolution.

Antigens, Bacterial↗
PubMed2004

Protein crystal growth on board Shenzhou 3: a concerted effort improves crystal diffraction quality and facilitates structure determination.

The crystallization of 16 proteins was carried out using 60 wells on board Shenzhou 3 in 2002. Although the mission was only 7 days, careful and concerted planning at all stages made it possible to obtain crystals of improved quality compared to their ground controls for some of the proteins. Significantly improved resolutions were obtained from diffracted crystals of 4 proteins. A complete data set from a space crystal of the PEP carboxykinase yielded significantly higher resolution (1.46A vs. 1.87A), I/sigma (22.4 vs. 15.5), and a lower average temperature factor (29.2A(2) vs. 42.9A(2)) than the best ground-based control crystal. The 3-D structure of the enzyme is well improved with significant ligand density. It has been postulated that the reduced convection and absence of macromolecule sedimentation under microgravity have advantages/benefits for protein crystal growth. Improvements in experimental design for protein crystal growth in microgravity are ongoing.

Crystallization↗
PubMed2002

Small-scale batch crystallization of proteins revisited: an underutilized way to grow large protein crystals.

Growth of high-quality crystals is a major obstacle in many structural investigations. In recent years, the techniques for screening crystals have improved dramatically, whereas the methods for obtaining large crystals have progressed more slowly. This is an important issue since, although many structures can be solved from small crystals with synchrotron radiation, it is far easier to solve and refine structures when strong data is recorded from large crystals. In an effort to improve the size of crystals, a strategy for a small-scale batch method has been developed that in many cases yields far larger crystals than attainable by vapor diffusion.

Bacterial Proteins↗
PubMed1996

Crystallization and preliminary diffraction data of a major pollen allergen. Crystal growth separates a low molecular weight form with elevated biological activity.

Group V major allergen Phl p 5b of timothy grass pollen induces allergic rhinitis and bronchial asthma in 90% of grass pollen-allergic patients. In addition to its allergenicity ribonuclease activity has recently been attributed to this 29-kDa protein. The allergen was expressed in Escherichia coli and subsequently purified. Spontaneous conversion of these preparations to a mixture of various forms with molecular sizes between 10 and 29 kDa was consistently observed. Surprisingly, crystals could be grown from this heterogenous preparation. Single crystals, redissolved and analyzed by SDS-polyacrylamide gel electrophoresis and immunoblot, yielded one distinct low molecular weight protein, which was identified by amino acid sequencing as the C-terminal 13-kDa portion of the allergen. Histamine release assays with single crystal solutions using basophils of an allergic patient demonstrated allergenicity comparable with that of the holo-allergen. By contrast, RNase activity of the crystallized C-terminal form was 23 times higher than that of the full-length parent allergen. Crystals were used to collect preliminary diffraction data; the space group was evaluated to I4122 with cell dimensions of a = 87.7 A, b = 87.7 A, and c = 59.6 A. We conclude that preferential crystal growth of the 13-kDa form is indicative of a compact conformation of this particular C-terminal portion of the allergen. Thus, we show here that protein crystallization is not only a prerequisite for structural analyses, but it also can provide a unique separation technique to localize the functional domain of a major allergen.

Allergens↗
PubMed1991

The effect of biological crystals and human serum on the rate of formation of crystals of monosodium urate monohydrate in vitro.

A simple, reproducible method of measuring monosodium urate monohydrate (urate) crystal formation in the presence of biological materials in vitro is described. The method allows both seeded and unseeded crystal formation to be examined. Urate seed crystals markedly promoted urate crystal growth whereas the presence of hydroxyapatite or calcium pyrophosphate dihydrate crystals had a minimal effect on crystal formation. Serum promoted urate crystal formation in a concentration-dependent fashion, the effect probably being due to enhancement of nucleation.

Adult↗
PubMed1995

Calcium pyrophosphate crystal deposition disease and other crystal deposition diseases.

"Tumoral" calcium pyrophosphate dihydrate (CPPD) crystal deposition in the ligamentum flavum is rare and can lead to compression myeloradiculopathy in the cervical spine and to spinal canal stenosis in the lumbar spine. CPPD crystal deposition disease is rarely associated with Bartter's syndrome and hypomagnesemia. Intramuscular corticotropin has proved effective in the treatment of acute episodes of pyrophosphate arthritis in patients with multiple medical illnesses in whom nonsteroidal anti-inflammatory drugs are contraindicated. IgG binding to CPPD crystals enhances neutrophil activation (by increasing intracellular cytoplasmic calcium levels) and seems to play a greater role in pyrophosphate than in urate crystal-induced inflammation. Transforming growth factor-beta 1 stimulates intracellular pyrophosphate generation by articular chondrocytes. The effect is inhibited by probenecid, an anion transport blocker, through interfering with the active transport of intracellular pyrophosphate to cartilage matrix where crystals form. Calcific tendinitis associated with underlying cortical bone erosions is an uncommon manifestation of apatite crystal deposition disease. Closed-needle tidal irrigation proved beneficial in two patients with Milwaukee shoulder syndrome. Two patients with nodular subcutaneous cholesterol crystal deposition are described.

Arthritis↗
PubMed2002

The Biological Macromolecule Crystallization Database: crystallization procedures and strategies.

The Biological Macromolecule Crystallization Database (BMCD) archives crystallization data from published reports for all forms of biological macromolecules that have produced crystals suitable for X-ray diffraction studies. The information includes the crystallization conditions, crystal data, comments about the crystallization procedure and information on the biological macromolecule or biological macromolecule complex. Crystallization procedures, including fast screens and more general procedures, can be developed effectively using this web-based resource (http://wwwbmcd.nist.gov:8080/bmcd/bmcd.html).

Crystallization↗
PubMed2004

Crystallization and preliminary analysis of active nitroalkane oxidase in three crystal forms.

Nitroalkane oxidase (NAO), a flavoprotein cloned and purified from Fusarium oxysporum, catalyzes the oxidation of neutral nitroalkanes to the corresponding aldehydes or ketones, with the production of H2O2 and nitrite. In this paper, the crystallization and preliminary X-ray data analysis of three crystal forms of active nitroalkane oxidase are described. The first crystal form belongs to a trigonal space group (either P3(1)21 or P3(2)21, with unit-cell parameters a = b = 103.8, c = 487.0 A) and diffracts to at least 1.6 A resolution. Several data sets were collected using 2theta and kappa geometry in order to obtain a complete data set to 2.07 A resolution. Solvent-content and Matthews coefficient analysis suggests that crystal form 1 contains two homotetramers per asymmetric unit. Crystal form 2 (P2(1)2(1)2(1); a = 147.3, b = 153.5, c = 169.5 A) and crystal form 3 (P3(1) or P3(2); a = b = 108.9, c = 342.5 A) are obtained from slightly different conditions and also contain two homotetramers per asymmetric unit, but have different solvent contents. A three-wavelength MAD data set was collected from selenomethionine-enriched NAO (SeMet-NAO) in crystal form 3 and will be used for phasing.

Crystallization↗
PubMed1998

Crystallization and preliminary X-ray analysis of thiaminase I from Bacillus thiaminolyticus: space group change upon freezing of crystals.

Thiaminase I (Mr = 42 100) from B. thiaminolyticus, expressed in E. coli, has been crystallized by the vapor-diffusion method. Three crystal forms, two of which grew from 0.1 M sodium acetate (pH = 4.6), 0.2 M ammonium sulfate and 30%(w/v) PEG 2000, have been examined by X-ray analysis. One crystal form diffracted to 2.5 A at room temperature, was orthorhombic, and had unit-cell edges of a = 87.7, b = 120.5 and c = 76.7 A with space group P212121. A self-Patterson map showed a strong peak indicating noncrystallographic translational pseudosymmetry with (u, v, w) = (0.03, 0.0, 0.5). When these crystals were frozen at liquid-nitrogen temperatures, a second crystal form was observed which had unit-cell dimensions a = 85.5, b = 117.5 and c = 36.6 A with space group P21212. A third crystal form grew from 0.1 M Tris (pH = 8.5), 0.2 M sodium acetate trihydrate and 28%(w/v) PEG 6000 to produce orthorhombic crystals of space group P212121 with cell edges of a = 114.4, b = 123.1 and c = 92.5 A.

Alkyl and Aryl Transferases↗
PubMed2006

Crystallization and preliminary characterization of three different crystal forms of human saposin C heterologously expressed in Pichia pastoris.

The amphiphilic saposin proteins (A, B, C and D) act at the lipid-water interface in lysosomes, mediating the hydrolysis of membrane building blocks by water-soluble exohydrolases. Human saposin C activates glucocerebrosidase and beta-galactosylceramidase. The protein has been expressed in Pichia pastoris, purified and crystallized in three different crystal forms, diffracting to a maximum resolution of 2.5 A. Hexagonal crystals grew from 2-propanol-containing solution and contain a single molecule in the asymmetric unit according to the Matthews coefficient. Orthorhombic and tetragonal crystals were both obtained with pentaerythritol ethoxylate and are predicted to contain two molecules in the asymmetric unit. Attempts to determine the respective crystal structures by molecular replacement using either the known NMR structure of human saposin C or a related crystal structure as search models have so far failed. The failure of the molecular-replacement method is attributed to conformational changes of the protein, which are known to be required for its biological activity. Crystal structures of human saposin C therefore might be the key to mapping out the conformational trajectory of saposin-like proteins.

Crystallization↗
PubMed2004

Phosphoglyceride (PG) crystal deposition disease: a novel acquired disease in which PG crystals are deposited in injured soft tissue and bone with phospholipid metabolism disturbance.

The clinical history and crystal characteristics of three published cases and three new cases of phosphoglyceride (PG) crystal deposition disease of soft tissues and bones were compared. All patients (age range, 51-64 years) were generally healthy without a genetic background of congenital immunodeficiency or lipidosis. Foreign body granulomas grew slowly, predominantly at postoperative or repeat injection lesions. In two cases, crystals were deposited in multiple locations, and in one case, lipophage accumulations were found in the bone marrow. The crystals characteristically dissolved in acetic acid with oxygen gas formation, easily dissolved in alkalis and showed positive staining for PG by the gold hydroxamic acid method. All crystals examined by infrared microscopy, mass spectrometry and X-ray microanalysis showed similar results, supporting the theory that the crystals were PG. Phosphoglyceride deposition disease is a lipid metabolic disorder in which PG crystals are slowly deposited, predominantly in injured soft tissues, forming foreign body granulomas. The diagnosis can be based on histological characteristics. The prognosis is favorable, although some cases showed systemic depositions with repetitions. Lysosomal phosphoglyceride metabolism in macrophages might be affected.

Bone Marrow↗
PubMedDate not supplied

Preparation of large crystals of photoactive yellow protein for neutron diffraction and high resolution crystal structure analysis.

The exact positions of all the hydrogen atoms in photoactive yellow protein (PYP) is important for understanding the molecular mechanism of the photoreaction because the protonation/deprotonation of certain amino acid residues and rearrangements in the hydrogen bond network are involved in the conformational changes of PYP. Neutron crystallography is one of the most effective methods to determine the hydrogen positions. However, a large crystal is required for neutron crystallography because a neutron-incident flux is quite limited. In addition, the crystal should be grown from heavy water to reduce the incoherent background from hydrogen. We prepared a large crystal of PYP (dimensions: 1.5 x 0.7 x 0.7 mm3) for neutron crystallography using ammonium sulfate with sodium chloride. The obtained large crystal gave X-ray diffraction spots up to 0.84 angstroms. Although some of the hydrogen atoms could be observed in the high resolution X-ray crystal structure, functionally important hydrogen atoms were impossible to see, indicating the importance of neutron crystallography. Thus, we optimized the crystallization conditions with heavy water and successfully obtained neutron diffraction spots up to 2.1 angstroms with the crystal in D2O.

Bacterial Proteins↗
PubMed2005

[Co-expression of crystal protein gene cry26Aa and cry28Aa has an ability to form parasporal crystal inside exosporium in Bacillus thuringiensis subsp. finitimus].

Parasporal crystal in Bacillus thuringiensis subsp. finitimus T02 forms within the exosporium and remains attached to the spore after mother cell lysis, which leads to spore-crystal connection. According to the crystal protein gene sequence in B. thuringiensis subsp. finitimus, cry26 and cry28 were cloned from strain T02 by PCR amplification and transformed into the crystal negative Bacillus thuringiensis strain BMB171 by shuttle vectors, alone or in combination together. Crystal can be observed inside of exosporium when co-expression of these two genes. But crystal mainly formed outside of exosporium when they expressed alone. This suggests interaction between of the two crystal proteins may be involved in enclosure.

Bacillus thuringiensis↗