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Crystallization studies of the catalytic subunit of cAMP-dependent protein kinase: crystals of murine recombinant catalytic subunit and a mutant, Cys 343----Ser, diffract to 2.7 A resolution.

The recombinant mouse catalytic subunit of cAMP-dependent protein kinase, expressed and purified from E. coli, has been successfully cocrystallized as a binary complex with an inhibitor peptide and as a ternary complex with an inhibitor peptide and MgATP. In contrast to the catalytic subunit obtained from porcine heart, the recombinant catalytic subunit lacks a myristoyl group at the amino terminus and differs in sequence at nine positions out of 350 amino acids. The catalytic activities of the two enzymes, however, are nearly identical. Both enzymes cocrystallized with a 20-amino-acid inhibitor and MgATP; however, the porcine-heart enzyme crystallized in a hexagonal space group (P6(1)22) while the recombinant murine catalytic subunit crystallized in an orthorhombic space group (P2(1)2(1)2(1), a = 73.70, b = 76.26, c = 80.74 A). The orthorhombic crystals of the recombinant catalytic subunit exhibit the best diffraction characteristics of all catalytic subunit crystals obtained so far: 2.7 A resolution. Unlike the mammalian porcine-heart enzyme, no crystals of the recombinant apo-enzyme were obtained under the same crystallization conditions. These results are consistent with earlier conclusions that the catalytic subunit exists in at least two distinct conformational states and furthermore suggests that the inhibitor peptide alone is sufficient to induce the major conformational changes that distinguish the two states. A mutant form of the catalytic subunit where Cys343 was replaced with Ser was also cocrystallized with the 20-amino-acid peptide inhibitor and MgATP, and resulted in an orthorhombic crystal isomorphous to crystals of the unmutated enzyme with a similar diffraction of 2.7 A.

Amino Acid Sequence↗

Comparative analysis of space-grown and earth-grown crystals of an aminoacyl-tRNA synthetase: space-grown crystals are more useful for structural determination.

Protein crystallization under microgravity aims at benefiting from the quasi-absence of convection and sedimentation to favor well ordered crystal nucleation and growth. The dimeric multidomain enzyme aspartyl-tRNA synthetase from Thermus thermophilus has been crystallized within dialysis reactors of the Advanced Protein Crystallization Facility in the laboratory on earth and under microgravity aboard the US Space Shuttle. A strictly comparative crystallographic analysis reveals that the crystals grown in space are superior in every respect to control crystals prepared in otherwise identical conditions on earth. They diffract X-rays more intensely and have a lower mosaicity, facilitating the process of protein structure determination. Indeed, the electron-density map calculated from diffraction data of space-grown crystals contains considerably more detail. The resulting three-dimensional structure model at 2.0 A resolution is more accurate than that produced in parallel using the data originating from earth-grown crystals. The major differences between the structures, including the better defined amino-acid side chains and the higher order of bound water molecules, are emphasized.

Amino Acyl-tRNA Synthetases↗

Crystallization of the collagen-like polypeptide (PPG)10 aboard the International Space Station. 2. Comparison of crystal quality by X-ray diffraction.

Crystals of the collagen-like polypeptide (PPG)(10) were obtained within the Advanced Protein Crystallization Facility on board the International Space Station, during the STS-105/STS-108 mission. The duration of this mission was such to ensure that the crystallization process had reached its end. Crystals were grown both in the presence and in the absence of agarose gel, to compare the quality of the crystals obtained from these different environments. As a result, crystals grown in the absence of agarose on Earth as well as in microgravity showed X-ray diffraction up to 1.15 A. The intensity/sigma ratio was slightly higher for microgravity grown crystals. Crystals grown in agarose gel, both in microgravity and on ground, showed a comparable diffraction power, with a resolution limit of 1.45 A.

Collagen↗

Physical aspects of protein crystal growth investigated with the Advanced Protein Crystallization Facility in reduced-gravity environments.

The physicochemical aspects of protein crystallization in reduced-gravity environments ( micro g) have been investigated with the Advanced Protein Crystallization Facility during six space missions. This review summarizes the results, dealing with the mechanisms of nucleation and crystal growth and with the quality of the crystals that were obtained under reduced gravity as well as under normal gravity on earth. Statistical analyses of the experimental data strongly support the fact that micro g has a positive effect on crystallization and on crystal quality. A comparison of experiments and theories of protein crystallization in reduced-gravity environments is presented. Recommendations for improving the performance of protein crystallization experiments in micro g and on earth are discussed.

Animals↗

Crystallization and preliminary X-ray diffraction studies of two different crystal forms of the lipase 2 isoform from the yeast Candida rugosa.

The yeast Candida rugosa produces several closely related lipases which show a high degree of sequence identity (between 77 and 88% for pairs of proteins). Despite this high sequence identity, they exhibit markedly different substrate specificities, indicating that subtle structural differences may produce significant functional changes. Isoform 2 (lip2) has been crystallized using the hanging-drop vapour-diffusion method at 291 K. Diffraction-quality crystals have been obtained from two different experimental conditions (designated A and B, respectively). Type A crystals belong to space group P1 and have unit-cell parameters a = 62.15, b = 91.14, c = 108.46 A, alpha = 90.78, beta = 106.31, gamma = 86.91 degrees; type B crystals are monoclinic with a nearly hexagonal topology, with unit-cell parameters a = 116.11, b = 225.55, c = 116.06 A, beta = 119.89 degrees, and belong to space group P2(1). Diffraction data were collected to a resolution of 1.97 A at a synchrotron facility from type A crystals and to 2.65 A on an in-house rotating-anode generator from type B crystals. Whereas the triclinic crystal reveals monomeric lip2, the monoclinic crystal contains dimeric lip2.

Candida↗

Post-crystallization treatments for improving diffraction quality of protein crystals.

X-ray crystallography is the most powerful method for determining the three-dimensional structure of biological macromolecules. One of the major obstacles in the process is the production of high-quality crystals for structure determination. All too often, crystals are produced that are of poor quality and are unsuitable for diffraction studies. This review provides a compilation of post-crystallization methods that can convert poorly diffracting crystals into data-quality crystals. Protocols for annealing, dehydration, soaking and cross-linking are outlined and examples of some spectacular changes in crystal quality are provided. The protocols are easily incorporated into the structure-determination pipeline and a practical guide is provided that shows how and when to use the different post-crystallization treatments for improving crystal quality.

Cross-Linking Reagents↗

Assessment of a preliminary solubility screen to improve crystallization trials: uncoupling crystal condition searches.

The utility of a preliminary solubility screen has been assessed on ten test proteins. It is proposed that maximizing the protein solubility prior to crystal setups is likely to improve crystal growth. In crystallization setups, drops of a protein solution are mixed with various crystallization solutions which are then allowed to equilibrate. The protein solutions usually contain a salt and buffer which are present as a constant in all crystal screens. The propensity for crystallization, driven by three components of sparse-matrix screens, the buffers, salts and precipitating agents, could potentially be masked by the components of the protein solution. Ten test proteins were dissolved in a standard buffer (100 mM NaCl, 50 mM Tris-HCl pH 7.5) and in customized optimal buffers determined to maximize solubility. The proteins were then subjected to the Index (Hampton Research) 96-well sparse-matrix crystal screen and to a precipitant/precipitant-additive screen described here. Five of the ten proteins studied showed twofold to fourfold increases in the saturation level from standard to optimal buffer, two showed slight improvement and three showed a slight decrease. Microcrystals were obtained for all proteins and optimal buffer increased the appearance of crystals for eight of the ten proteins.

Chemical Precipitation↗

Crystal-growth kinetics of protein single crystals along capillary tubes in the gel-acupuncture technique.

In attempts to obtain protein crystals of a sufficient size for structural studies, lack of knowledge of the physicochemical properties of protein solutions and of their crystal-growth behaviour lead to a bottleneck for drug design as well as for X-ray crystallography. Most formal investigations on crystal-growth phenomena have been focused on equilibrium studies, where the protein is soluble, and on the kinetics of crystal growth, which is related to both nucleation and crystal-growth phenomena. The aim of this work is to measure the crystal-growth rate along a capillary tube used as a growing cell. These experiments were carried out using the gel-acupuncture technique [García-Ruiz et al. (1993). Mater. Res. Bull. 28, 541-546; García-Ruiz & Moreno (1994). Acta Cryst. D50, 484-490; García-Ruiz & Moreno (1997). J. Cryst. Growth, 178, 393-401]. Crystal-growth investigations took place using lysozyme and thaumatin I as standard proteins. The maximum average growth rate obtained in the lower part of the capillary tube was about 35 A s-1 and the minimum average growing rate in the upper part of the capillary tube was about 8 A s-1. The crystal-growth rate as a function of the supersaturation was experimentally estimated at a constant height along the capillary tube.

Chemical Precipitation↗

Improved crystals of Thermus thermophilus prolyl-tRNA synthetase complexed with cognate tRNA obtained by crystallization from precipitate.

The complex between Thermus thermophilus prolyl-tRNA synthetase (ProRSTT) and its cognate tRNA has been crystallized using two different isoacceptors of tRNA(Pro). Similar bipyramidal crystals of the complexes of ProRSTT with the two different tRNA(Pro) isoacceptors grow within two weeks from 32% saturated ammonium sulfate solution. They belong to space group P4(3)2(1)2, with unit-cell parameters a = 143.1, b = 143.1, c = 228.6 A. The crystals diffract weakly to a maximum resolution of 3.1 A. Superior quality crystals were obtained by growing slowly from precipitate over 5-6 months. These are of the same space group but have slightly altered unit-cell parameters, a = 140.8, b = 140.8, c = 237.0 A. These crystals diffract more strongly to at least 2.8 A resolution and a complete data set to 2.85 A resolution has been collected from a single crystal. Comparison of the packing in the two crystal forms shows that domain flexibility contributes to the presence of different crystal contacts in the two forms.

Amino Acyl-tRNA Synthetases↗

[Studies on calcium oxalate crystal formation in urolithiasis. Multi-regressive analysis of urinary CaOx crystalline volumes and the effects of urinary various substances on CaOx crystal formation].

Because human urine contains various substances which can affect each other, it is quite difficult to clarify the mechanism of formation of calcium oxalate (CaOx) crystal in urine. The authors recently determined CaOx crystalline content and the concentrations of other substances in urine specimens from patients with urolithiasis and healthy volunteers, and subjected the data to multi-regressive analysis for the purpose of assessing the effect of these urinary substances on CaOx crystal formation. 1. In analysis of urine from patients with urolithiasis, the partial correlation coefficients of CaOx crystal formation with oxalic acid, sodium, calcium, uric acid magnesium were 0.67, 0.28, 0.18, and -0.10, respectively. The formula of regression was as follows: Amount of CaOx crystal (X 10(6) microns3/ml) = 3.59 X 10(-2) Ox (mM/L) + 4.72 X 10(-3) Ca (mM/L) + 4.52 X 10(-3) Na (mM/L) + 2.51 X 10(-4) UA (mM/L) -2.39 X 10(-2) Mg (mM/L) -1.65. The multiple correlation coefficient was 0.759. Thus, in patients with urolithiasis, urinary crystal formation was most dependent on the oxalic acid level, sodium, calcium, and uric acid were found to promote crystal formation, while magnesium to suppress it. 2. In analysis of urine from healthy volunteers, the partial correlation coefficients of CaOx crystal formation with oxalic acid and inorganic phosphorus were 0.51 and -0.24, respectively. The formula of regression was as follows: Amount of CaOx crystal (X 10(6) microns3/ml) = 1.91 X 10(-2) Ox (mM/L) -3.43 X 10(-4) P (mM/L) +0.29 The multiple correlation coefficient was 0.525.(ABSTRACT TRUNCATED AT 250 WORDS)

Calcium↗

Crystal-induced neutrophil activation. VII. Involvement of Syk in the responses to monosodium urate crystals.

The inflammatory response in acute gouty arthritis is in large part a result of the interaction between neutrophils and monosodium urate (MSU) crystals. The tyrosine kinase Syk, which has been largely associated with the phagocytic response by Fc receptors and with spreading mediated by integrins, has been identified as one of the major proteins tyrosine-phosphorylated in human neutrophils upon stimulation by MSU crystals and is known to be mediated in part by the Fc receptor, CD16. This has led to the present examination of the implication of Syk in the activation pathways used by MSU crystals. The tyrosine-phosphorylation patterns induced by MSU crystals and by the ligation of CD16 were inhibited by piceatannol, which, conversely, only slightly delayed but did not diminish the peak of tyrosine phosphorylation induced by cross-linking CD32 or by the addition of fMet-Leu-Phe. Moreover, piceatannol inhibited the activity of Syk as monitored by in vitro kinase assays, by its in situ tyrosine phosphorylation, and by its activity toward exogenous substrates after stimulation by MSU crystals. We also measured the impact of piceatannol on the mobilization of calcium, the production of superoxide anions, and the activity of PLD stimulated by MSU crystals. We noted a distinct inhibition of all these responses by piceatannol. Finally, the morphological changes observed in neutrophils as characteristic of MSU crystal internalization were diminished significantly by piceatannol. The results obtained show that Syk plays a critical and central role in the signal-transduction pathways called upon by MSU crystals subsequent to their interaction with human neutrophils.

Adult↗

Use of a fusion protein to obtain crystals suitable for X-ray analysis: crystallization of a GST-fused protein containing the DNA-binding domain of DNA replication-related element-binding factor, DREF.

Crystals of glutathione-S-transferase (GST)-fused protein containing the DNA-binding domain of DNA replication-related element-binding factor, DREF, were obtained under crystallization conditions similar to those for GST. Preliminary X-ray crystallographic analysis revealed that crystals of the GST-fused protein belong to space group P6(1)22 or P6(5)22 with unit cell dimensions a = b = 140.4 A, c = 93.5 A and gamma = 120 degrees, having one molecule in the crystallographic asymmetric unit. The crystals diffract to 2.5 A resolution. The cell dimensions are related to those of GST crystals thus far reported. Crystallization of the DNA-binding domain that was cleaved from the fused protein by thrombin was also carried out using several methods under numerous conditions, but efforts to produce well-ordered large crystals were unsuccessful. A possible application of GST-fusion proteins for small target proteins or domains to obtain crystals suitable for X-ray structure determination is proposed.

Crystallography, X-Ray↗

Usefulness of dual-head coincidence gamma camera with thick NaI crystals for nuclear oncology: comparison with dedicated PET camera and conventional gamma camera with thin NaI crystals.

AIM: A comparative study of the images obtained with a dual-head coincidence gamma camera with thick NaI crystals (19 mm), a dedicated PET camera with BGO crystals and a conventional gamma camera with thin NaI crystals (9.5 mm) was conducted to clarify the clinical feasibility of a dual-head coincidence gamma camera with thick NaI crystals. METHODS: FDG images of 27 patients with malignant tumors were obtained by means of a dual-head coincidence gamma camera with thick NaI crystal and a dedicated PET camera with BGO crystals. The images of bone scintigraphy in 10 cancer patients obtained with the dual-head coincidence gamma camera were compared with those taken by a conventional dual-head gamma camera with thin NaI crystals. RESULTS: Patient-basis sensitivity in 27 patients with neoplasms and lesion-basis sensitivity of the dual-head coincidence gamma camera and the dedicated PET camera were 74.1% and 85.2% (n.s.), 66.7% and 72.2% (n.s.), respectively. The tumor to background FDG uptake ratio derived from the coincidence gamma camera was significantly lower than that derived from the dedicated PET camera (mean +/- s.d.; 3.48 +/- 3.77 vs. 8.12 +/- 8.92, p < 0.0001), but the tumor to background FDG uptake ratio obtained with both methods correlated well (r = 0.84, p < 0.001). Similar whole body bone scans were obtained with the dual-head coincidence gamma camera and the conventional dual-head gamma camera in all 10 patients. CONCLUSION: These results suggest that the dual-head coincidence gamma camera with thick NaI crystals has potentially high clinical applicability for community hospitals.

Adult↗

Crystal-induced membrane damage: hydroxyapatite crystal-induced hemolysis of erythrocytes.

Microcrystals of hydroxyapatite cause severe membrane damage in human erythrocytes, as is evident from the strong hemolysis that is caused by these crystals. Hemolysis by hydroxyapatite crystals is time and concentration dependent, and is preceded by aggregation of erythrocytes. Polyvinylpyridine-N-oxide, a strong hydrogen acceptor, has no inhibiting effect on hydroxyapatite-induced hemolysis. This suggest that the mechanism of action of these crystals is different from that of urate crystals and silica particles, where hydrogen bonding interaction is supposed to be important. Negatively charged macromolecules, such as dextran sulfate, heparin, and polyglutamic acid, inhibit hydroxyapatite crystal-induced hemolysis, suggesting that positive charges, probably located on the crystals, play an important role in the membrane-damaging effect of these crystals. The structures with which these positive charges interact remain to be determined because removal of negative charges from the erythrocytes by treatment with neuraminidase does not affect crystal-induced hemolysis.

Adenosine Triphosphate↗

Successful prediction of the hydrogen bond network of the 3-oxo-12alpha-hydroxy-5beta-cholan-24-oic acid crystal from resolution of the crystal structure of deoxycholic acid and its three 3,12-dihydroxy epimers.

Crystal structures of p-xylene-crystallized deoxycholic acid (3alpha,12alpha-dihydroxy-5beta-cholan-24-oic acid) and its three epimers (3beta,12alpha-; 3alpha,12beta-; and 3beta,12beta-) have been solved. Deoxycholic acid forms a crystalline (P21) complex with the solvent with a 2:1 stoichiometry whereas crystals of the three epimers do not form inclusion compounds. Crystals of the 3beta,12beta-epimer are hexagonal, whereas the 3alpha,12beta-and 3beta,12alpha-epimers crystallize in the P2(1)2(1)2(1) orthorhombic space group. The three hydrogen bond sites (two hydroxy groups, i. e. O3-H, and O12-H, and the carboxylic acid group of the side chain, O24bO24a-H) simultaneously act as hydrogen bond donors and acceptors. The hydrogen bond network in the crystals was analyzed and the following sequences have been observed: two chains (abcabc... or acbacb... ) and two rings (abc or acb), which constitute a complete set of all the possible sequences which can be drawn for an intermolecular hydrogen bond network formed by three hydrogen bond donor/acceptor sites forming crossing hydrogen bonds. The orientation of O3-H (alpha or beta) determines the sequence of the acceptor and the donor groups involved in the pattern: O24a --> O12 --> O3 --> O24b when it is alpha and O24a --> O3 --> O12--> O24B when it is beta. These observations were used to predict the hydrogen bond network of p-xylene-crystallized 3-oxo,12alpha-hydroxy-5beta-cholan-24-oic acid. This compound has two hydrogen bond donor and three potential hydrogen bond acceptor sites. According to the previous sequence set, this compound should crystallize in the monoclinic P21 system, should form a complex with the solvent, O24b should not participate in the hydrogen bond network, and the chain sequence O24a --> O12 --> O3 would be followed. All predictions were confirmed experimentally.

Cholic Acids↗

Absolute asymmetric photocyclization of isopropylbenzophenone derivatives using a cocrystal approach involving single-crystal-to-single-crystal transformation.

Absolute asymmetric photocyclization of isopropylbenzophenone derivatives was achieved by means of a cocrystal approach. Three chiral salt crystals formed by carboxylic acid derivatives with achiral amines could be prepared by spontaneous crystallization. In the M-crystal of 4-(2,5-diisopropylbenzoyl)benzoic acid with 2,4-dichlorobenzylamine, a twofold helical arrangement occurs in a counterclockwise direction to generate the crystal chirality. Conversely, the clockwise helix exists alone in the P-crystal. Irradiation of the M-crystal at >290 nm caused highly enantioselective Norrish type II cyclization to give the (R,R)-cyclopentenol, (R)-cyclobutenol, and (R)-hydrol in a 6:3:1 molar ratio, resulting in successful absolute asymmetric synthesis, while irradiation at around 350 nm afforded the (R,R)-cyclopentenol as the sole product. The reaction proceeded via single-crystal-to-single-crystal transformation, and therefore the reaction path producing the (R,R)-cyclopentenol could be traced by X-ray crystallographic analysis before and after irradiation.

Journal Article↗

Crystal-liquid crystal binary phase diagrams.

We propose a new theoretical scheme for the binary phase diagrams of crystal-liquid crystal mixtures by a combination of a phase field model of solidification, the Flory-Huggins theory for liquid-liquid mixing and Maier-Saupe-McMillan (FH-MSM) model for nematic and smectic liquid crystal orderings. The phase field theory describes the crystal phase transition of anisotropic organic crystal and/or side chain liquid crystalline polymer crystals while the FH-MSM model explains isotropic, nematic and smectic-A phase transitions. Self-consistent calculations reveal several possible phase diagram topologies of the binary crystal-liquid crystal mixtures. The calculated phase diagrams were found to accord well to the reported experimental results.

Journal Article↗

Epitaxial growth of a colloidal hard-sphere hcp crystal and the effects of epitaxial mismatch on crystal structure.

We demonstrate the epitaxial growth of hard-sphere hcp and double hcp crystals using a surface pattern that directly dictates the stacking sequence. A detailed three-dimensional analysis based on real-space measurements is performed on crystal structure as a function of template-crystal mismatch, which demonstrates the possibilities of colloidal epitaxy as a model system for studying the effects of a patterned substrate on crystal structure. Perfect template-induced hcp-crystal growth occurs at an isotropically deformed template. At deformed lattices we observe growth of a non-close-packed superstructure and of a perfect (100)-aligned fcc crystal. Small mismatches lead to increased out-of-plane displacements followed by a structural breakup in "crystal" grains where particle positions in successive layers are strictly periodic and "defect" grains where these positions are displaced with respect to each other. Large mismatches prevent crystallization in the surface layers. The volume fraction was found to vary drastically (up to about 20% ) as a function of template deformation.

Journal Article↗