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Crystallization of seed globulins from legumes.

Seeds contain large quantities of proteins and are therefore main food sources. In the last century, protein extracts of legume seeds were dialysed against distilled water and in some cases small crystals of pure protein appeared. However, those crystals were generally of poor quality with respect to X-ray diffraction. Recently, the crystallization of some of them was improved and the structures of two 7S globulins, phaseolin from Phaseolus vulgaris and canavalin from Canavalia ensiformis, have been determined at 3.0 and 2.6 A resolution, respectively. Efforts to improve the quality of the phaseolin crystals resulted in three new crystal forms which will be discussed in this paper. The only high-resolution X-ray analysis of a seed globulin from legumes is that of narbonin, a 2S protein from Vicia narbonensis. The crystal structure at 1.8 A shows a very compact packing in layers of molecules. The intermolecular contacts include salt bridges and hydrophobic clusters that might facilitate both the aggregation of the molecules and their crystallization. Because the seed globulins appear in large quantities in the protein bodies of the seeds, efficient packing of the molecules similar to the crystal packing can be assumed.

Journal Article↗

A new crystal form of bovine heart ubiquinol: cytochrome c oxidoreductase: determination of space group and unit-cell parameters.

Ubiquinol:cytochrome c oxidoreductase, the middle segment of the mitochondrial respiratory chain, is a multi-subunit transmembrane redox enzyme. The purified protein from beef heart mitochondria has been crystallized by three groups in three different forms, but progress toward a structure has been hampered by the limited order (resolution) of the crystals. It has been found that under certain conditions the enzyme crystallizes in a new form suitable for X-ray diffraction studies. These crystals belong to space group C222(1) in the orthorhombic system. The cell dimensions are a = 384, b = 118 and c = 177 A. These new crystals at present diffract to 3.8 A at best. This is not significantly better than hexagonal [P6(1(5))22] crystals grown, but the new crystals have the advantage of less spot overlap because of face-centered packing which results in systematic extinctions. More importantly, the availability of the same enzyme in multiple crystal forms may allow phase refinement and extension by the method of molecular replacement.

Journal Article↗

Human class II MHC molecule HLA-DR1: X-ray structure determined from three crystal forms.

The three-dimensional structure of the extracellular region of a 60 kDa class II major histocompatibility glycoprotein, HLA-DR1, was determined to 3.3 A by X-ray crystallography using three crystal forms, each containing two molecules per asymmetric unit. Phases were initially determined to 4.2 A using two crystal forms both containing DR1 from human lymphocytes complexed with a mixture of endogenous peptides. One of these crystal forms also contained a 28 kDa superantigen, Staphylococcus aureus enterotoxin B (SEB), bound to each DR1 molecule. Single-isomorphous replacement phasing followed by iterative two- and fourfold non-crystallographic real-space averaging between the two crystal forms resulted in 4.2 A resolution electron-density maps from which the paths of the polypeptides could be traced. Cryocrystallography and synchrotron radiation were then used to extend the resolution to 3.3 A for the two lymphocyte-derived crystal forms and for a third crystal form grown from DR1 produced in insect cells and complexed in vitro with a specific antigenic peptide. Iterative sixfold non-crystallographic real-space averaging resulted in an electron- density map into which 340 of 371 residues could be fit unambiguously. Crystal contacts and the existence of a parallel dimer of the DR1 alphabeta heterodimer in the three crystal forms are discussed.

Journal Article↗

A local approximation to supersaturation affords a useful coordinate transformation for the study of crystal growth.

Two of the most important experimental variables in the search for appropriate crystallization conditions are the initial concentrations of macromolecule and crystallizing agent. Previously, it has been suggested that the coordinate transformation { [crystallizing agent], [macromolecule] } --> { [macromolecule] x [crystallizing agent], [macromolecule]} be used to sample crystal growth conditions. Here, it is shown that this transformation is a special case of a generally applicable transformation. The initial supersaturation can be represented locally by a rectangular hyperbola involving multiples of the product of macromolecule and crystallizing agent concentrations. The coordinate system for the solubility diagram, ([crystallizing agent] versus [macromolecule]), can thus be transformed analytically to an alternative coordinate system in which the independent variables are local approximations to the initial supersaturation and the reservoir of soluble macromolecule available to feed a growing seed. In the new coordinate system the 'nucleation zone' is 'orthogonalized', so it can be sampled efficiently on a rectangular grid, with greater assurance that experiments will give rise to crystals. Moreover, since these new coordinate directions segregate fundamental effects on nucleation from effects on growth, using them in experimental designs should improve data analysis for response surface experiments.

Journal Article↗

A new crystal form of carboxypeptidase G2 from Pseudomonas sp. strain RS-16 which is more amenable to structure determination.

Carboxypeptidase G(2) is a zinc-dependent exopeptidase which has applications in cancer therapy. Crystallization of carboxypeptidase G(2), first achieved more than a decade ago, yields large crystals; however, problems with non-isomorphism between native crystals as well as failure to obtain any useful heavy-atom derivatives have precluded structure solution. A modification of the crystallization protocol leading to a promising new crystal form which diffracts beyond 3.0 A resolution on a rotating-anode source is now reported. These crystals are readily indexed on an apparent C-centred orthorhombic lattice with a = 81.35, b = 230.9 and c = 105.5 A, but the correct crystal system is monoclinic. The crystals have space group P2(1), with a = 81.35, b = 105.5, c = 122.4 A and beta = 109.3 degrees. There are two possible non-equivalent monoclinic indexings with these lattice constants. A partial native data set collected at the SRS, Daresbury, indicates that 1.9 A diffraction is attainable. Structure determination using MIR methods is in progress.

Journal Article↗

X-ray analysis of crystals of rat phosphatidylinositol-transfer protein with bound phosphatidylcholine.

Phosphatidylinositol-transfer protein (PITP) is a soluble, ubiquitously expressed, highly conserved protein encoded by two genes in humans, rodents and other mammals. A cDNA encoding the alpha isoform of the rat gene was expressed to high levels in Escherichia coli, the protein purified and the homogeneous protein used for crystallization studies. Crystals of rat PITP-alpha were obtained by vapor-diffusion techniques using the sitting-drop method. Crystals grow within two weeks by vapor-diffusion techniques in the presence of polyethylene glycol 4000. Both crystal forms pack in the monoclinic space group P21. Crystal form I has unit-cell parameters a = 44.75, b = 74.25, c = 48.32 A and beta = 114.14 degrees. Unit-cell parameters for crystal form II are a = 47.86, b = 73.59, c = 80.49 A and beta = 98.54 degrees. Crystal form I has a Vm of 2.295 A3 Da-1 and an estimated solvent content of 46.4% with one molecule per asymmetric unit, while crystal form II has a Vm of 2.196 A3 Da-1 and an estimated solvent content of 44.0%, assuming two molecules per asymmetric unit.

Animals↗

Crystallization and preliminary X-ray analysis of a novel Kunitz-type kallikrein inhibitor from Bauhinia bauhinioides.

A Kunitz-type protease inhibitor (BbKI) found in Bauhinia bauhinioides seeds has been overexpressed in Escherichia coli and crystallized at 293 K using PEG 4000 as the precipitant. X-ray diffraction data have been collected to 1.87 A resolution using an in-house X-ray generator. The crystals of the recombinant protein (rBbKI) belong to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 46.70, b = 64.14, c = 59.24 A. Calculation of the Matthews coefficient suggests the presence of one monomer of rBbKI in the asymmetric unit, with a corresponding solvent content of 51% (VM = 2.5 A3 Da(-1)). Iodinated crystals were prepared and a derivative data set was also collected at 2.1 A resolution. Crystals soaked for a few seconds in a cryogenic solution containing 0.5 M NaI were found to be reasonably isomorphous to the native crystals. Furthermore, the presence of iodide anions could be confirmed in the NaI-derivatized crystal. Data sets from native and derivative crystals are being evaluated for use in crystal structure determination by means of the SIRAS (single isomorphous replacement with anomalous scattering) method.

Bauhinia↗

Iterative crystal efficiency calculation in fully 3-D PET.

The calculation of the intrinsic efficiency of individual crystals is one of the steps needed to obtain accurate images of the radioisotope distribution in positron emission tomography (PET). These efficiencies can be computed by comparing the number of coincidence counts obtained when the crystals are equally illuminated by the same source. However, because the number of coincidence counts acquired for one crystal also depends on the efficiency of the other crystals in coincidence, most methods of crystal efficiency calculation need to assume that the influence of the other crystals is negligible. If there are large crystal efficiency variations, this approximation may lead to systematic errors. We have recently implemented an iterative method for a single ring of detectors that does not rely on this assumption. In this paper, we describe a fully three-dimensional (3-D) iterative method that better exploits the sensitivity of the tomograph and allows reduced acquisition times or the use of narrow energy windows. We compare the performance of the iterative method (single-ring and extended to fully 3-D) with noniterative techniques for different acquisition times of a uniform cylinder. Two different energy windows were used to assess the performance of each method with different levels of variations of crystal efficiency. The results showed that the iterative methods are more accurate when large efficiency variations exist and that only the fully 3-D methods provided good efficiency estimates with very low duration scans. We, thus, conclude that iterative fully 3-D methods provide the best estimations and can be used in a larger range of situations than can the other methods tested.

Algorithms↗

The technical development of crystals and oscillators in China and their market situation.

In recent years the manufacture of and demand for crystals and oscillators in China have been increasing quickly because of the development of industries, communications, science, transportation, and electronic techniques. This paper introduces the manufacture, research, and characteristics of the technical development of crystals and oscillators in the last ten years in China. To meet the demand from industry, science, and other markets, the number of companies that produce and research crystals and oscillators has increased from several to more than 300 in the last 20 years. Manufacturing technology and equipment have also improved. For marketing and technical reasons, more than 75% of the companies manufacture mainly 49 micro, 49 micros, and microm crystals. Now more and more companies plan to build production lines to make cold-weld crystals and other precision crystals, and at least two companies have already built their production lines. Most of the precision crystals are AT-cut but some are SC-cut. Integrated TCXOs and DTCXOs have been made by different companies, and the frequency-temperature stability of them is from +/- 2 ppm to +/- 0.5 ppm in a wide temperature range. Specifications of some OCXOs are almost the same as those of foreign OCXOs. The main design techniques in China are experimental. However, in recent years, specially designed software has been developed for oscillator design, and advanced instrumentation and equipment are used. The market situation for crystals and oscillators has increased.

Journal Article↗

Determination of the true congruent composition for LiTaO3 single crystals using the LFB ultrasonic material characterization system.

The true congruent composition for LiTaO3 single crystals was determined by measuring the velocities of leaky surface acoustic waves (LSAWs) with the line-focus-beam ultrasonic material characterization (LFB-UMC) system for two 42 degrees YX-LiTa3s crystal ingots. The congruent composition determined here was 48.460 Li2O-mol%, corresponding to the LSAW velocity (42 degrees YX-LiTaO3) of 3125.3 m/s, and the absolute relationship between the LSAW velocity and chemical composition was obtained. Simulations on the variation of the melt and crystal compositions in a mass production of 100 crystals were conducted as a function of the composition of the starting material around the congruent composition. The result showed that the distributions of the melt and crystal compositions within and among the crystals varied largely with the material composition, providing the relationship of the material composition with the maximum composition variation for the 100 crystals. Based on these results, we verified the relationships between the tolerance of the material composition variation and the tolerances for the SH-type SAW velocity, LSAW velocity, and Curie temperature. The material composition needs to be constrained to within +/- 0.007 Li2O-mol% around the congruent composition to mass-produce the crystals with reliable homogeneity, satisfying the tolerance of +/- 0.01% in the SAW velocity. Furthermore, a guideline for the specification of reliable piezoelectric SAW-device wafer substrates was presented with the accurate interrelationships among the chemical composition ratio, LSAW velocity, and Curie temperature.

Journal Article↗

Biodegradation of crystal violet by the white rot fungus Phanerochaete chrysosporium.

Biodegradation of crystal violet (N,N,N',N',N'',N''-hexamethylpararosaniline) in ligninolytic (nitrogen-limited) cultures of the white rot fungus Phanerochaete chrysosporium was demonstrated by the disappearance of crystal violet and by the identification of three metabolites (N,N,N',N',N''-pentamethylpararosaniline, N,N,N',N''-tetramethylpararosaniline, and N,N',N''-trimethylpararosaniline) formed by sequential N-demethylation of the parent compound. Metabolite formation also occurred when crystal violet was incubated with the extracellular fluid obtained from ligninolytic cultures of this fungus, provided that an H2O2-generating system was supplied. This, as well as the fact that a purified ligninase catalyzed N-demethylation of crystal violet, demonstrated that biodegradation of crystal violet by this fungus is dependent, at least in part, upon its lignin-degrading system. In addition to crystal violet, six other triphenylmethane dyes (pararosaniline, cresol red, bromphenol blue, ethyl violet, malachite green, and brilliant green) were shown to be degraded by the lignin-degrading system of this fungus. An unexpected result was the finding that substantial degradation of crystal violet also occurred in nonligninolytic (nitrogen-sufficient) cultures of P. chrysosporium, suggesting that in addition to the lignin-degrading system, another mechanism exists in this fungus which is also able to degrade crystal violet.

Basidiomycota↗

Dissolution of calcium pyrophosphate crystals by polyphosphates: an in vitro and ex vivo study.

OBJECTIVE: To determine the dissolving ability (DA) of linear pentasodium tripolyphosphate (PSTP), cyclic trisodium metaphosphate (TSMP), polymeric sodium metaphosphate (SMP) on synthetic crystals of calcium pyrophosphate dihydrate (CPPD) and on crystalline aggregates of menisci from patients with chondrocalcinosis (CC). METHODS: Synthetic CPPD crystals were mixed with phosphate buffered saline (PBS), which contained the different polyphosphates, for one hour at 37 degrees C. The calcified menisci were obtained from the knees of four female patients with CPPD disease who underwent total arthroscopic meniscectomy for degenerative meniscal lesions. Meniscal cryosections and fragments were incubated in SMP (15 mg/ml PBS) at 37 degrees C for one hour and 24 hours, respectively. Histological evaluation on meniscal samples after polyphosphate incubation was carried out by ordinary transmitted light microscopy and polarised light microscopy. The dissolution of CPPD crystals by polyphosphates was assessed by atomic absorption spectroscopy, which determined the amount of calcium liberated from synthetic crystals and meniscal fragments. Cytotoxicity of SMP was evaluated by tetrazolium salt assay and by an ultrastructural study on cultured chondrocytes. RESULTS: SMP and PSTP showed higher DA on CPPD crystals than TSMP. Analysis of the DA values at increasing concentrations of SMP showed that a concentration of 15 mg/ml completely dissolved 2.0 mg CPPD crystals. The solution of meniscal CPPD crystals showed a significant increase of calcium concentration after three hours and 24 hours of SMP incubation (p=0.0001; Kruskal-Wallis analysis of variance) compared with fragments incubated in PBS control solution. Macroscopic and microscopic evaluation of meniscal specimens showed a notable reduction of CPPD deposits. A 50% inhibitory dose on cultured chondrocytes was reached at the maximum concentration of SMP used in this work (15 mg/ml); ultrastructural analysis did not show morphological alterations in the treated cells. CONCLUSION: The results of this study indicate that linear polyphosphates are effective in dissolving both synthetic and ex vivo CPPD crystal aggregates. This suggests a potential therapeutic use for these molecules in the treatment of symptomatic CC.

Aged↗

Glass transition and the origin of poly(p-phenylene sulfide) secondary crystallization.

The effect of low temperature cold-crystallization on quenched poly(p-phenylene sulfide) (PPS) amorphous phase behaviour was systematically investigated by differential scanning calorimetry (DSC) and dynamic mechanical thermal analysis (DMTA) over the entire range of the process, from its early stage to the end. For the first time a well resolved double glass transition of partially cold-crystallized samples was evidenced. A T(g) steady increase was observed during the primary crystallization process, due to the reduction of amorphous chain segmental mobility imposed by the growing rigid phase. A shift of the relaxation temperature of about 10 degrees C was recorded at the end of the primary crystallization process. As the secondary crystallization takes place a new glass transition appears at higher temperature. For longer annealing time the lower T(g) disappears while the intensity of the upper one increases. The upper temperature glass transition of semi-crystalline PPS is explained as a consequence of the PPS secondary cold-crystallization process. In the light of the thermal and dynamic mechanical results, an interpretation is given of step-wise double crystallization, evidenced in non-isothermal cold-crystallization experiments carried out at low heating rate and followed by means of FT-IR techniques.

Journal Article↗

Observation on intranuclear crystal and nucleolar size at different stages of cell differentiation in the midgut epithelium of several insects.

Based on an inverse size relationship between nuclear crystal and nucleolus in different cells it has been postulated by several authors that the crystal develops from nucleolar materials. The purpose of the present paper is to investigate the validity of this argument. Intranuclear proteinaceous crystals appear in differentiating midgut cells of Gyrinus marinus and Tenebrio molitor. In an autoradiographic study we have previously demonstrated in these two species that the crystals do not develop from nucleolar materials. However, an inverse relationship with regard to size is observed between these 2 structures during the cell differentiation: the cross-sectional area of the nucleolus decreases when the cross-sectional area of the crystal increases. But a decrease in size of the nucleolus is also observed during the differentiation of the midgut cells of Gyrinus natator where the crystals are not present. Consequently an inverse size relationship cannot be a sufficient argument to postulate that intranuclear crystals and nucleoli are interconvertible structures; decrease in size of the nucleolus is not related to development of the intranuclear crystal.

Animals↗

In situ observation of the four-step dehydration process of the 1 beta-methylcarbapenem antibiotic CS-834 crystal by X-rays.

The 1 beta-methylcarbapenem antibiotic CS-834 takes six crystalline forms depending on ambient conditions. The X-ray powder diffraction revealed that the dihydrate crystal (B2-form) was changed to the monohydrate (B1-form) through the intermediate form (B2'-form). The monohydrate form was then changed to the dehydrate (B0-form) through the intermediate B1'-form. The progress of the dehydration along the needle axis (c-axis) was observed under a microscope. When a single crystal of the B2-form was mounted on a diffractometer and the humidity was reduced, the crystal was gradually changed to the various dehydration forms with retention of the single crystal. The crystals of B2- to B0-forms form isostructures to each other except the solvent water molecules. In the crystal structure of the B1-form, the pivaloyloxymethyl moiety is disordered. One is nearly similar to that of the B2-form, while another is similar to that of the B0-form. Each crystal structure consists of a columnar arrangement of CS-834 along the c-axis, and the water molecules are located between the columns and form a characteristic hydrogen bond network. When the water molecules leave the crystal, the columns slide slightly following the slight conformational change in the pivaloyloxymethyl groups and are connected by another type of hydrogen bond network. Such a rearrangement of the hydrogen bond network should be a motive force of the phase change to the next step due to the dehydration. Since the hydrogen bond network extends along the c-axis, the dehydration proceeds along the c-axis as observed microscopically.

Anti-Bacterial Agents↗

[Mechanism of the inhibitory effect of pranoprofen on sodium urate crystal-induced inflammation].

The mechanism of the inhibitory effect of pranoprofen on sodium urate crystal-induced inflammation was investigated with several inflammatory parameters using leucocytes stimulated with sodium urate crystals in vitro. At 10(-5) M, pranoprofen tended to inhibit the production of chemotactic factor in guinea pig polymorphonuclear leucocytes (PMNL) stimulated with sodium urate crystals and at 10(-4) M, significantly inhibited it. At 10(-3) M and 10(-4) M, it potentiated the chemotaxis of guinea pig PMNL. Furthermore, it inhibited the production of superoxide anion (O2-) in guinea pig PMNL stimulated with sodium urate crystals, with an IC50 value of 5.0 X 10(-4) M, comparable to that of indomethacin. At 10(-3) M, it inhibited the release of beta-glucuronidase stimulated by sodium urate crystals. From doses as low as 10(-6) M, it inhibited dose-dependently the production of PGE2-like substance by the phagocytosis of sodium urate crystals by rat peritoneal leucocytes, with an IC50 value of 7.5 X 10(-6) M. These results suggest that in inhibiting the production of PGE2 stimulated by sodium urate crystals, pranoprofen shows an inhibitory effect on sodium urate crystal-induced inflammation.

Animals↗

[Effects of alminoprofen on sodium urate crystal-induced inflammation].

Effects of alminoprofen (AP), a non-steroidal anti-inflammatory agent, were investigated using several experimental gouty models. AP (3-30 mg/kg, p.o.) dose-dependently inhibited urate crystal-induced rat paw edema. AP (3-30 mg/kg, p.o.) inhibited the accumulation of exudate and decreased the total counts of leukocytes and the amount of PGE2 in a dose-dependent manner in sodium urate crystal-induced pleuritic rats. AP (0.3-10 mg/kg, p.o.) showed a dose-related analgesic activity on the pain response in sodium urate crystal-induced arthritic rats. AP (10(-5)-10(-3)M) inhibited the sodium urate crystal-induced beta-glucuronidase release from guinea pig neutrophils at more than 10(-4) M. AP (10(-5)-10(-3)M) did not inhibit the sodium urate crystal-induced production of O2- from guinea-pig neutrophils. AP (10(-6)-10(-4) M) inhibited dose-dependently the chemotaxis of leukocytes induced by chemotactic factors from guinea pig neutrophils stimulated with sodium urate crystals. AP (10(-6)-10(-4) M) inhibited the sodium urate crystal-induced production of PGE2 from rat peritoneal leukocytes in a dose-related manner. These results suggest that AP has a potent anti-inflammatory and analgesic activity in sodium urate crystal-induced inflammations, and these effects are exerted through its combined inhibitions of PGE2 synthesis, leukocyte chemotaxis and lysosomal enzyme release.

Animals↗

Threshold effects for resistance to optical damage and nonvolatile holographic storage properties in In:Mn:Fe:LiNbO3 crystals.

The threshold concentration for In2O3 was found in In:Mn:Fe:LiNbO3 crystals by measurement of the infrared spectra of the crystals. The resistance of the In:Mn:Fe:LiNbO3 crystals to optical damage is characterized by changes in photoinduced birefringence as well as by distortion of the transmitted beam pattern. The resistance increases remarkably when the concentration of In2O3 exceeds its threshold. The resistance to optical damage of a In(3.0 mol. %):Mn:Fe:LiNbO3 crystal is 2 orders of magnitude higher that of a Mn:Fe:LiNbO3 crystal. The dependence of defects on the resistance to optical damage of the In:Mn:Fe:LiNbO3 crystals is discussed in detail. Nonvolatile holographic storage was achieved for all crystals, and the sensitivity of the In(3.0 mol. %):Mn:Fe:LiNbO3 crystal is much higher than that of the others.

Journal Article↗