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PubMed2006

A model-based approach for mining membrane protein crystallization trials.

MOTIVATION: Membrane proteins are known to play crucial roles in various cellular functions. Information about their function can be derived from their structure, but knowledge of these proteins is limited, as their structures are difficult to obtain. Crystallization has proved to be an essential step in the determination of macromolecular structure. Unfortunately, the bottleneck is that the crystallization process is quite complex and extremely sensitive to experimental conditions, the selection of which is largely a matter of trial and error. Even under the best conditions, it can take a large amount of time, from weeks to years, to obtain diffraction-quality crystals. Other issues include the time and cost involved in taking multiple trials and the presence of very few positive samples in a wide and largely undetermined parameter space. Therefore, any help in directing scientists' attention to the hot spots in the conceptual crystallization space would lead to increased efficiency in crystallization trials. RESULTS: This work is an application case study on mining membrane protein crystallization trials to predict novel conditions that have a high likelihood of leading to crystallization. We use suitable supervised learning algorithms to model the data-space and predict a novel set of crystallization conditions. Our preliminary wet laboratory results are very encouraging and we believe this work shows great promise. We conclude with a view of the crystallization space that is based on our results, which should prove useful for future studies in this area.

Algorithms↗

PubMed1977

Preliminary morphological and X-ray diffraction studies of the crystals of the DNA cetyltrimethylammonium salt.

Double-stranded DNA molecules (molecular weight 2.5 X 10(5) - 5 X 10(5) daltons) have been crystallized from water-salt solutions as cetyltrimethylammonium salts (CTA-DNA). Variation of crystallization conditions results in a production of different types of CTA-DNA crystals: spherulits, dendrites, needle-shaped and faceted rhombic crystals, the latter beeing up to 0.3 mm on a side. X-ray diffraction data indicate that DNA molecules in the crystals form a hexagonal lattice which parameters vary slightly with the morphological type of the crystal. Comparison of the melting curves of the DNA preparation before and after crystallization suggests that DNA molecules are partially fractionated in the course of crystallization. Crystals of the CTA-DNA-proflavine complex have also been obtained.

Cetrimonium Compounds↗

PubMed2003

Designing proteins to crystallize through beta-strand pairing.

Inherent difficulties in growing protein crystals are major concerns within structural biology and particularly in structural proteomics. Here, we describe a novel approach of engineering target proteins by surface mutagenesis to increase the odds of crystallizing the molecules. To this end, we have exploited our recent triad-hypothesis using proteins with crystallographically defined beta-structures as the principal models. Crystal packing analyses of 182 protein structures belonging to 21 different superfamilies implied that the propensities to crystallize could be engineered into target proteins by replacing short segments, 5-6 residues, of their beta-strands with 'cassettes' of suitable packing motifs. These packing motifs will generate specific crystal packing interactions that promote crystallization. Key features of the primary and tertiary structures of such packing motifs have been identified for immunoglobulins. Further, packing motifs have been engineered successfully into six model antibodies without disturbing their capabilities to be produced, their immunoreactivity and their overall structure. Preliminary crystallization analyses have also been performed. Taken together, the procedures outline a rational protocol for crystallizing proteins by surface mutagenesis. The importance of these findings is discussed in relation to the crystallization of proteins in general.

Animals↗

PubMed1995

A quantitative study of the phagocytosis of urate crystals in the synovial fluid of asymptomatic joints of patients with gout.

The objective of this study was to determine whether monosodium urate (MSU) crystals are phagocytosed in the synovial fluid (SF) of the asymptomatic joints of patients with gout. SF samples were obtained from 20 asymptomatic knees of 19 different patients. Cell and differential counts were done. Intracellular MSU crystals were identified by ordinary and polarizing light microscopy. We found that in 19 out of the 20 SF samples intracellular MSU crystals have been found. A mean of 22.55% [confidence interval (CI) 13.92, 31.18; range 0-62] of all the cells contained intracellular MSU crystals. The majority of the cells which contained intracellular crystals were mononuclear cells (MC), and polymorphonuclear (PMN) leucocytes containing intracellular crystals accounted only for 0.5% (CI 0, 1.05; range 0-5) of the total. The total cell count was 527 cells/mm3 (CI 226, 828, range;: 30-2670). Poor correlation was found between the percentage of cells with intracellular crystals and both the total cell count (r = -0.22) and the percentage of PMN leucocytes (r = -0.26). We conclude that cells containing phagocytosed MSU crystals--generally mononuclear cells--are a regular finding in the SF of asymptomatic joints of patients with gout. This finding indicates that other factors besides intra-articular interaction between crystals and cells are necessary to produce arthritis in gouty patients.

Crystallization↗

PubMed1993

Birefringent (calcium oxalate) crystals in thyroid diseases. A clinicopathological study with possible implications for differential diagnosis.

To elucidate the nature and significance of calcium oxalate crystals in the pathologic thyroid, we used polarized light microscopy to review 357 thyroid lesions. Under polarized light, calcium oxalate crystals had brilliant birefringence, and they were invariably identified within the colloid of follicles. The highest prevalence of crystals (87.9%) was in nodular goiters; they were also found in 60.0% of follicular adenomas and 33.3% of follicular carcinomas. The prevalence of crystals in papillary carcinomas was very low (5.4%). Therefore, the overall prevalence was 69.4% in benign nodules and 7.6% in malignant nodules. A heavy deposit of crystals was seen only in benign nodules except for one case of follicular carcinoma. Graves' disease, focal thyroiditis, and subacute thyroiditis showed low prevalence: 25.0, 46.9, and 40.0%, respectively. In cases of toxic nodules, the crystals were sparsely identified within nodules, but abundantly observed in surrounding inactive tissues. Immunohistochemistry for thyroid hormones confirmed that the crystals tended to appear in inactive follicles. On tissue x-ray film, the crystals appeared as microcalcifications. As a result of these findings, we suggest that examinations of crystals are likely to be useful in the differential diagnosis of thyroid diseases and in possible estimations of the functional state of lesions.

Adenoma↗

PubMed2003

Inhibitors of articular calcium crystal formation.

The coexistence of calcium phosphate and calcium pyrophosphate crystals in osteoarthritis is a well-described phenomenon. In addition to deposition in articular cartilage, the crystals induce numerous changes to biochemical parameters in the surrounding fluid. This survey discusses crystal-inhibitor interactions whereby defining the molecular structure of crystals assists in an optimal inhibitor design. Crystal growth studies in the presence and absence of a test compound can generate data on crystal face changes. Together with knowledge of the inhibitors' molecular structure, computer modeling can portray crystal-inhibitor interactions. Few inhibitors have been tested in both in vitro and in vivo phases. One exception is phosphocitrate. This compound inhibits both the development of specific calcium crystals and crystal-induced intracellular changes. Animal studies confirm a strong action on pathologic calcification. The recently described phosphocitrate in a mixed calcium and sodium salt, yet to be tested in a guinea pig osteoarthritis model, appears to be an even more powerful inhibitor.

Animals↗

PubMed1995

Matrix modulates uptake of calcium oxalate crystals and cell growth of renal epithelial cells.

Handling of urinary crystals by renal epithelial and medullary interstitial cells may play an important role in the pathogenesis of renal stones and associated renal scarring. We examined the effects of calcium oxalate monohydrate (CaOM) crystals on the proliferative activity of renal tubular cells (opossum kidney) and renal medullary interstitial cells in culture. We also studied the impact of altered extracellular matrix on cell proliferation as well as on uptake of crystals by epithelial cells. Epithelial cells incubated with CaOM showed greater (p < 0.05) growth when compared with untreated cells (control, 10.5 +/- 1.1 versus CaOM, 16.6 +/- 1.6 x 10(6) cells per dish). the CaOM crystal-cell interaction also enhanced proliferation of interstitial cells (at 48 hours, control, 3.3 +/- 0.2 versus CaOM, 4.2 +/- 0.1 x 10(6) cells per dish, p < 0.02; at 72 hours, control, 3.6 +/- 0.3 versus 5.5 +/- 0.4 x 10(6) cells per dish, p < 0.01). Collagen, a constituent of extracellular matrix, inhibited (p < 0.01) proliferation of epithelial cells. Semiconfluent epithelial cells grown on collagen gels showed greater (p < 0.01) uptake of 45CaOM crystals when compared with uptake by cells grown on either uncoated (control) or albumin-coated plastic dishes (control, 979.9 +/- 51.1, albumin, 876.4 +/- 28.3, collagen gel, 1502.5 +/- 103.8 cpm per well). Epithelial cells grown to confluence on collagen gels also showed enhanced (p < 0.05) uptake of 45CaOM crystals. Reflectance microscopy as well as ultrastructural studies revealed intracellular localization of CaOM crystals. These results indicate that CaOM crystals stimulate the growth of both epithelial and interstitial cells. Enhanced growth of interstitial cells may also lead to increased synthesis of extracellular matrix. The latter may further modulate crystal uptake as well as cell growth of adjacent epithelial cells. These findings may be important in the development of nephrolithiasis and associated interstitial scarring.

Animals↗

PubMed1996

Biliary sludge: can ultrasound reliably detect the presence of crystals in bile?

OBJECTIVE: To determine the accuracy of routine gallbladder ultrasound in the detection of crystals in bile. METHODS: Preoperative ultrasonography was performed in 40 patients undergoing elective cholecystectomy. Bile was aspirated at operation and examined microscopically for the presence and quantity of crystals. RESULTS: Six patients had echogenic bile, five of whom had large numbers of crystals at microscopy, and one only a few crystals. Thirty-four patients had hypoechoic bile, nine had large numbers of crystals and 25 of these had few or no crystals at microscopy. For those patients with echogenic bile (hyper- or isoechoic) the sensitivity for detection of large numbers of crystals was 5/14 (35.7%) with a specificity of 25/26 (96%). However, if the bile was hypoechoic the sensitivity was 9/14 (65%). CONCLUSION: For those patients with echogenic bile, ultrasound is highly specific for the detection of crystals, although the sensitivity is low. By contrast, those patients with hypoechoic bile at ultrasound would need a further investigation to exclude the presence of crystals.

Adolescent↗

PubMed2004

Effect of gallbladder mucin on the crystallization of cholesterol in bile.

OBJECTIVES: Mucin is supposed to accelerate the crystallization of cholesterol in model bile while studies in native human gallbladder bile revealed conflicting results. METHODS: Therefore, we determined the relation of mucin concentration and cholesterol crystal observation time in gallbladder bile of 73 patients with cholesterol and mixed and 21 patients with pigment stones. In addition, bile samples of 20 patients with cholesterol gallstones were supplemented with either 0 (control) or 0.5-4.0 mg/ml purified bovine mucin or human mucin isolated from gallbladder bile, to study the effect of variable mucin concentrations on the crystallization of cholesterol. RESULTS: Rapid nucleating biles (</= 4 days, n = 59) showed higher mucin concentrations (0.73 +/- 0.1 mg/ml vs 0.43 +/- 0.07 mg/ml) than biles with longer (> 4 days, n = 35) cholesterol crystal observation times (P < 0.05), but no correlation between mucin concentration and cholesterol crystal observation time was observed. Supplementation experiments with bovine purified mucin (up to 4.0 mg/ml) showed no significant effect on the total amount of newly formed cholesterol crystals within 21 days. However, higher amounts of newly formed cholesterol crystals were seen in bile samples supplemented with human mucin in comparison to negative controls. CONCLUSIONS: Our results demonstrate a dose-dependent effect of human but not of bovine gallbladder mucin on the formation of cholesterol monohydrate crystals in gallbladder bile of patients with cholesterol stones. Therefore, studies of cholesterol crystallization in model bile systems may be valuable but should always be confirmed in native gallbladder bile as the more physiological effector system.

Adult↗

PubMed2005

Geometrical parameterization of the crystal chemistry of P6(3)/m apatites: comparison with experimental data and ab initio results.

Experimental structure refinements and ab initio simulation results for 18 published, fully ordered P6(3)/m (A;{\rm I}_4)(A;{\rm II}_6)(BO4)6X2 apatite end-member compositions have been analyzed in terms of a geometric crystal-chemical model that allows the prediction of unit-cell parameters (a and c) and all atom coordinates. To an accuracy of +/- 0.025 A, the magnitude of c was reproduced from crystal-chemical parameters characterizing chains of ...-A(II)-O3-B-O3-A(II)-... atoms, whereas that of a was determined from those describing (A(I)O6)-(BO4) polyhedral arrangements. The c/a ratio could be predicted to +/-0.2% using multi-variable functions based on geometric crystal-chemical model predictions, but could not be ascribed to the adjustment of a single crystal-chemical parameter. The correlations observed between algebraically independent crystal-chemical parameters representing the main observed polyhedral distortions reveal them as the minimum-energy solution to accommodate misfit components within this flexible structure type. For materials with given composition, good agreement (within +/- 0.5-2.0%) of ab initio crystal-chemical parameters was observed with only those from single-crystal refinements with R </= 4.0%. Agreement with single-crystal work with R > 4.0% was not as good, while the scatter with those from Rietveld refinements was considerable. Accordingly, ab initio cell data, atomic coordinates and crystal-chemical parameters were reported here for the following compositions awaiting experimental work: (Zn,Hg)10(PO4)6(Cl,F)2, (Ca,Cd)10(VO4)6Cl2 and (Ca,Pb,Cd)10(CrO4)6Cl2.

Apatites↗

PubMed2001

Crystallization of Clonorchis sinensis 26 kDa glutathione S-transferase and its fusion proteins with peptides of different lengths.

A Clonorchis sinensis 26 kDa glutathione S-transferase (CsGST) and its fusion proteins containing 14 and 48 amino-acid peptides at the N-terminus have been crystallized using polyethylene glycol monomethylether 550 as a precipitant. Crystals of the three proteins show very similar crystal properties: they diffract to at least 2.3 A resolution and belong to the orthorhombic space group P2(1)2(1)2(1). The unit-cell parameters of CsGST crystals were a = 66.64 (1), b = 68.91 (1), c = 123.41 (2) A, which are very close to those of the crystals of the two fusion proteins. In addition, CsGST fusion proteins containing varying extents of N-terminal-extended peptides are incorporated into a crystal, indicating that the extended peptides have little effect on crystal packing. These results suggest that the crystallization system of CsGST/peptide fusion protein may be generally applicable to obtain crystals of small peptides.

Amino Acid Sequence↗

PubMed2001

Structure of tetragonal hen egg-white lysozyme at 0.94 A from crystals grown by the counter-diffusion method.

Very high quality crystals of tetragonal hen egg-white lysozyme were grown in the Advanced Protein Crystallization Facility (APCF) on board the Space Shuttle using a modified free-interface diffusion (FID) reactor designed ad hoc to have a longer diffusion path. This design allows the performance of true counter-diffusion experiments. Crystals were obtained under the classical chemical conditions defined 50 y ago with NaCl as a crystallizing agent and acetate pH 4.5 as a buffer. Counter-diffusion crystallization allows a "physical" instead of chemical optimization of growth conditions: indeed, this method screens for the best supersaturation conditions in a single trial and yields crystals of very high quality. A complete diffraction data set was collected at atomic resolution from one of these crystals using synchrotron radiation at the DESY-EMBL beamlines. The overall R(merge) on intensities in the resolution range 31-0.94 A was 5.2% and the data were 98.9% complete. Refinement was carried out with the programs CNS and SHELX97 to a final crystallographic R factor of 12.26% for 72 390 reflections. A mean standard uncertainty in the atomic positions of 0.024 A was estimated from inversion of blocked least-squares matrices. 22 side chains show alternate conformations and the loop 59-75 adopts in the same crystal packing two conformations that were observed for either triclinic or tetragonal lysozyme in previous high-resolution studies. In addition to 255 water molecules, the crystallizing agent (one hexacoordinated sodium ion and five chloride anions) participates in the ordered lysozyme hydration shell.

Amino Acids↗

PubMed2002

Thaumatin crystallization aboard the International Space Station using liquid-liquid diffusion in the Enhanced Gaseous Nitrogen Dewar (EGN).

This paper reports results from the first biological crystal-growth experiment on the International Space Station (ISS). Crystals of thaumatin were grown using liquid-liquid diffusion in Tygon tubing transported in the Enhanced Gaseous Nitrogen Dewar (EGN). Different volume ratios and concentrations of protein and precipitant were used to test different adaptations of the vapor-diffusion crystallization recipe to the liquid-liquid diffusion method. The EGN warmed up from 77 to 273 K in about 4 d, about the same time it took to warm from 273 to 293 K. The temperature within the EGN was 293-297 K for the majority of the experiment. Air gaps that blocked liquid-liquid diffusion formed in the tubes. Nonetheless, crystals were grown. Synchrotron diffraction data collected from the best space-grown crystal extended to 1.28 A, comparable to previous studies of space-grown thaumatin crystals. The resolution of the best ground-control crystal was only 1.47 A. It is not clear if the difference in diffraction limit arises from factors other than crystal size. Improvements in temperature control and the elimination of air gaps are needed, but the results show that the EGN on the ISS can be used to produce space-grown crystals that diffract to high resolution.

Crystallization↗

PubMed2002

Crystallization of the collagen-like polypeptide (PPG)10 aboard the International Space Station. 1. Video observation.

Single chains of the collagen model polypeptide with sequence (Pro-Pro-Gly)(10), hereafter referred to as (PPG)(10), aggregate to form rod-shaped triple helices. Crystals of (PPG)(10) were grown in the Advanced Protein Crystallization Facility (APCF) both onboard the International Space Station (ISS) and on Earth. The experiments allow the direct comparison of four different crystallization environments for the first time: solution in microgravity ((g), agarose gel in (g, solution on earth, and gel on earth. Both on board and on ground, the crystal growth was monitored by a CCD video camera. The image analysis provided information on the spatial distribution of the crystals, their movement and their growth rate. The analysis of the distribution of crystals reveals that the crystallization process occurs as it does in batch conditions. Slow motions have been observed onboard the ISS. Different to Space-Shuttle experiment, the crystals onboard the ISS moved coherently and followed parallel trajectories. Growth rate and induction time are very similar both in gel and in solution, suggesting that the crystal growth rate is controlled by the kinetics at the interface under the used experimental conditions. These results provide the first data in the crystallogenesis of (PPG)(10), which is a representative member of non-globular, rod-like proteins.

Collagen↗

PubMed2003

Improved three-dimensional growth of manganese superoxide dismutase crystals on the International Space Station.

Manganese superoxide dismutase was crystallized in microgravity with 35 PCAM experiments (Protein Crystallization Apparatus for Microgravity) on the ISS (International Space Station) from 5 December 2001 to 19 April 2002. Crystals were very large in size and could easily be seen by eye. Crystals with 0.45 x 0.45 mm cross-sections and of up to 3 mm in length were obtained in several drops: an 80-fold increase in crystal Volume compared with the largest earth-grown crystal. A smaller crystal (0.15 x 0.30 mm in cross-section and 1.6 mm in length) was soaked in cryoprotectant and placed in a cryoloop. Diffraction data were collected at 100 K at the BioCARS bending-magnet beamline. The space group was C222(1), with unit-cell parameters a = 100.64, b = 107.78, c = 179.82 A. Diffraction spots to 1.26 A resolution were observed. Unfortunately, the high-resolution diffraction degraded owing to radiation damage and the resolution limit for the complete data set was 1.35 A. It is anticipated that increasing the crystal Volume and diffraction limit through microgravity crystal growth will enable several types of technically challenging structure determinations.

Crystallization↗

PubMed2003

Crystallization and preliminary X-ray analysis of swine vesicular disease virus (SVDV).

Three different crystal forms of the swine vesicular disease virus (SVDV), isolate SPA/2/'93, were obtained by the hanging-drop vapour-diffusion technique using ammonium sulfate and sodium/potassium phosphate as precipitants. Monoclinic crystals, space group C2, with unit-cell parameters a = 473.7, b = 385.3, c = 472.8 A, beta = 100.4 degrees, contain one virus pArticle in the crystal asymmetric unit and diffract to 3.0 A resolution. A second type of crystals had a cubic morphology and diffracted beyond 2.6 A resolution. These crystals belong to a primitive orthorhombic space group, with unit-cell parameters a = 319.6, b = 353.8, c = 377.7 A, and contain half a virus pArticle in the asymmetric unit. A third type of crystals, with a prismatic shape and belonging to space group I222, was also obtained under similar crystallization conditions. These latter crystals, with unit-cell parameters a = 318.3, b = 349.9, c = 371.7 A, diffract to at least 3.0 A resolution and contain 15 protomers per asymmetric unit; this requires that three perpendicular crystal twofold axes coincide with three of the viral pArticles' dyad axes.

Ammonium Sulfate↗

PubMed2003

Crystallization and initial X-ray diffraction of BtuB, the integral membrane cobalamin transporter of Escherichia coli.

BtuB, the cobalamin transporter from Escherichia coli, has been overexpressed, purified and crystallized. The purified protein was solubilized in n-octyl tetraoxyethylene (C(8)E(4)) and was crystallized using sitting-drop vapor diffusion with PEG 3350 and magnesium acetate as precipitants (pH 6.5). Two crystal forms have been obtained. Crystal type I belongs to space group P3(1)21, with unit-cell parameters a = b = 81.6, c = 210.0 A, alpha = beta = 90, gamma = 120 degrees. Crystal type II belongs to space group P3(1)21, with unit-cell parameters a = b = 81.6, c = 226.0 A, alpha = beta = 90, gamma = 120 degrees. Each crystal form contains a monomer in the asymmetric unit. Diffraction for crystal type I extends to 2.0 A and diffraction for crystal type II extends to 2.7 A. Both crystal forms are suitable for structure determination.

Bacterial Outer Membrane Proteins↗

PubMed2003

A manual nanoscale method for protein crystallization.

To overcome one of the major hurdles in three-dimensional crystal structure determination - the requirement for large quantities of purified material to grow crystals - crystallization methodologies have been developed that require only a total of 2-5 microl of a concentrated macromolecular solution to screen more than 100 conditions. These procedures employ a circular slide containing an array of 25 wells designed for crystallization setups in the nanolitre volume range. These 'crystallization slides' fit into the wells of standard crystallization trays. These nanoscale crystallization approaches have been used to reproducibly obtain well diffracting crystals of three proteins, two that are being actively studied (glycerol kinase and NADH peroxidase) and one test protein (lysozyme), using only 40-350 microg (0.04-0.35 mg) of proteins to screen 100 conditions. These nanolitre crystallization methods are easily adapted for the typical laboratory, without the requirement of robotics or expensive equipment.

Crystallization↗