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At least 217 records · Page 12Linked to original sources
PubMed1997

Calcium crystal-associated diseases and miscellaneous crystals.

Calcium crystal-associated diseases are still a challenge in clinical and basic science. Advances in understanding crystal formation and dissolution and crystal participation in inflammation are reported here. Studies on different methods of identification are reviewed, emphasizing the need for accurate and reproducible ways to study and diagnose calcium crystal-associated diseases. Reports of uncommon presentations are also described, including a controlled study on calcification of the ligamenta flava of the spine and a study involving 19 years of clinical follow-up of families with hydroxyapatite chondrocalcinosis with spondyloepiphyseal dysplasia. Studies on miscellaneous crystals are few. Two recent reviews are described on cholesterol crystal embolization syndrome and cryocrystalglobulinemia.

Apatites↗
PubMed1988

A structural approach to pathological crystallizations. Gout: the possible role of albumin in sodium urate crystallization.

The interactions between sodium urate monohydrate (MSU) crystals and human serum albumin (HSA) were investigated in vitro in relation to the disease of gout. It was found that HSA accelerates (by up to ten times or even more) the nucleation of MSU crystals at a pH of more than 7.5, but only to a much lesser extent (1.2 times) at pH 7.0. Protein denaturation, as well as blocking exposed carboxylate groups on the protein, substantially reduced the nucleating effect. By use of immunofluorescence, immunogold labelling and crystal morphology studies, albumin was shown to interact preferentially with the (110) faces of MSU crystals. Taking these results into consideration, a mechanism is proposed whereby albumin stabilizes MSU crystal nuclei by interaction of structured carboxylate-containing protein domains with planes of the incipient crystal exposing sodium cation layers.

Crystallization↗
PubMed2005

Remarkable features in lattice-parameter ratios of crystals. II. Monoclinic and triclinic crystals.

The frequency distributions of monoclinic crystals as a function of the lattice-parameter ratios resemble the corresponding ones of orthorhombic crystals: an exponential component, with more or less pronounced sharp peaks, with in general the most important peak at the ratio value 1. In addition, the distribution as a function of the monoclinic angle beta has a sharp peak at 90 degrees and decreases sensibly at larger angles. Similar behavior is observed for the three triclinic angular parameters alpha, beta and gamma, with characteristic differences between the organic and metal-organic, bio-macromolecular and inorganic crystals, respectively. The general behavior observed for the hexagonal, tetragonal, orthorhombic, monoclinic and triclinic crystals {in the first part of this series [de Gelder & Janner (2005). Acta Cryst. B61, 287-295] and in the present case} is summarized and commented. The data involved represent 366 800 crystals, with lattice parameters taken from the Cambridge Structural Database, CSD (294 400 entries), the Protein Data Bank, PDB (18 800 entries), and the Inorganic Crystal Structure Database, ICSD (53 600 entries). A new general structural principle is suggested.

Crystallization↗
PubMed2000

Crystallization and preliminary X-ray diffraction data of mouse L-chain apoferritin crystals.

Crystals of recombinant mouse L-chain apoferritin were obtained by the hanging-drop technique using ammonium sulfate as precipitant. Two crystal forms were observed in the same drop. The crystals belong to either the P2 monoclinic or to the P42(1)2 tetragonal space group. The monoclinic crystals diffracted to beyond 2.4 A resolution but were systematically twinned, while the tetragonal crystals diffracted to beyond 2.9 A. These crystallization conditions in the absence of metal salts should facilitate the study of the interaction between L-chain ferritins and heavy metals, particularly the iron core.

Animals↗
PubMed2000

Crystallization and preliminary crystallographic analysis of a new crystal form of arylsulfatase A isolated from human placenta.

Depending on pH, arylsulfatase A exists in solution as a dimer or as an octamer. The enzyme isolated from human placenta was crystallized at pH 5.4 in a new crystal form with space group C2, unit-cell parameters a = 154.0, b = 190.3, c = 112.5 A, beta = 122.4 degrees and four subunits in the asymmetric unit. At pH 6.5-6.7, tetragonal crystals are obtained that are isomorphous to the known crystals of recombinant arylsulfatase A obtained at pH 5.0-5.4. The crystal structure of both forms was determined by the molecular-replacement method. The monoclinic crystals contain octamers of the same type as found in the tetragonal form.

Cerebroside-Sulfatase↗
PubMed2001

Crystallization and preliminary X-ray analysis of a DNA dodecamer containing 2'-deoxy-5-formyluridine; what is the role of magnesium cation in crystallization of Dickerson-type DNA dodecamers?

To investigate the role of divalent cations in crystal packing, four different crystals of a Dickerson-type dodecamer with the sequence d(CGCGAATXCGCG), containing 2'-deoxy-5-formyluridine at X, were obtained under several conditions with and without divalent cations. The crystal structures are all isomorphous. The octahedrally hydrated magnesium cations found in the major groove cement the two neighbouring duplexes along the b axis. In the Mg(2+)-free crystals, a five-membered ring of water molecules occupies the same position as the magnesium site and connects the two duplexes similarly to the hydrated Mg(2+) ion. It has been concluded that water molecules can take the place of the hydrated magnesium cation in crystallization, but the magnesium cation is more effective and gives X-ray diffraction at slightly higher resolution. In all four crystals, the 5-formyluracil residues form the canonical Watson-Crick pair with adenine residues.

Base Sequence↗
PubMed2001

Crystallization and preliminary crystallographic studies of five crystal forms of Escherichia coli L-asparaginase II (Asp90Glu mutant).

L-Asparaginase II from Escherichia coli with an Asp90Glu mutation in the active site has been crystallized in five polymorphic forms. Crystals of all polymorphs suitable for X-ray diffraction experiments were obtained by the vapour-diffusion method. Crystals of form I belong to the monoclinic system (space group C2), have unit-cell parameters a = 73.1, b = 133.1, c = 62.6 A, beta = 108.8 degrees and diffract to 2.27 A resolution. Three of the crystal forms are orthorhombic, with unit-cell parameters a = 225.4, b = 128.0, c = 62.6 A (form II, P2(1)2(1)2), a = 59.9, b = 71.2, c = 130.6 A (form III, primitive cell) and a = 73.8, b = 122.1, c = 124.2 A (form IV, P2(1)2(1)2(1) or P2(1)2(1)2); the crystals diffract to 2.33, 3.5 and 1.7 A, respectively. Polymorph V is trigonal, space group P3(1)21, with unit-cell parameters a = 123.1, c = 83.8 A; the crystals diffract to 2.65 A resolution.

Asparaginase↗
PubMed2002

From conventional crystallization to better crystals from space: a review on pilot crystallogenesis studies with aspartyl-tRNA synthetases.

Aspartyl-tRNA synthetases were the model proteins in pilot crystallogenesis experiments. They are homodimeric enzymes of Mr approximately 125 kDa that possess as substrates a transfer RNA, ATP and aspartate. They have been isolated from different sources and were crystallized either as free proteins or in association with their ligands. This review discusses their crystallisability with emphasis to crystal quality and structure determination. Crystallization in low diffusivity gelled media or in microgravity environments is highlighted. It has contributed to prepare high-resolution diffracting crystals with better internal order as reflected by their mosaicity. With AspRS from Thermus thermophilus, the better crystalline quality of the space-grown crystals within APCF is correlated with higher quality of the derived electron density maps. Usefulness for structural biology of targeted methods aimed to improve the intrinsic physical quality of protein crystals is highlighted.

Aspartate-tRNA Ligase↗
PubMed2004

Crystallization and preliminary X-ray analysis of pseudo-merohedrally twinned crystals of the full-length beta(2) subunit of the Kv1 K(+) channel from Rattus norvegicus.

The eukaryotic Kv1 voltage-gated K(+) channel is composed of four alpha subunits and four beta subunits. The full-length beta(2) subunit from Rattus norvegicus has been expressed in Esherichia coli, purified and then crystallized. A careful molecular-replacement study using the structure of the truncated beta(2) subunit reveals that the crystals are perfectly pseudo-merohedrally twinned. While the apparent space group of the crystals was P42(1)2, the real space group was shown to be P2(1)2(1)2, with unit-cell parameters a = 222.6, b = 222.6, c = 82.3 A. An asymmetric unit of the crystal contains two beta(2) tetramers (MW = 340 kDa). A data set was collected from a crystal to 2.0 A resolution, with 266 659 independent observations (93.0% complete) and R(merge) = 0.06. Although the crystals are perfectly twinned, they are still suitable for structural determination by molecular replacement using the truncated beta(2)-subunit structure.

Animals↗
PubMed1999

Improving the diffraction quality of MTCP-1 crystals by post-crystallization soaking.

Significant improvement in the resolution and quality of the X-ray diffraction of crystals of MTCP-1 protein was observed on post-crystallization soaking. The MTCP-1 crystals grown from 1.5 M ammonium sulfate diffracted to only 3.0 A resolution with some disorder in the diffraction. After post-crystallization soaking in a solution containing 2.0 M ammonium sulfate, the disorder was eliminated and diffraction extended to better than 2.0 A resolution. Both native and selenomethionine-enriched crystals demonstrated better diffraction after soaking for several months. This simple technique may be useful to improve the diffraction quality of protein crystals generally.

Ammonium Sulfate↗
PubMed1994

Crystallization and analyses of crystals of various chemotypes of R-form lipopolysaccharides from Salmonella spp.

Various chemotypes (Re, Rd2, Rd1P-, Rd1, RcP-, Rc, Rb3, Rb2, Rb1, and Ra) of R-form lipopolysaccharides (LPSs) of Salmonella spp. were crystallized by treatment with 70% ethanol containing 250 mM MgCl2, and crystals of the LPSs were observed electron microscopically and analyzed by electron diffraction and synchrotron X-ray diffraction. All the LPSs tested formed three-dimensional crystals showing very similar shapes; hexagonal plate, solid column, discoid, square or rectangular plate, lozenge plate and truncated hexangular or rectangular pyramid forms. Electron diffraction patterns from the hexagonal plate crystals of all these LPSs obtained by electron irradiation from the direction perpendicular to the basal plane showed that they consist of hexagonal lattices with the lattice constant of 4.62 A. The crystals of all the LPSs thus formed gave ring-like X-ray diffraction patterns because of their small sizes. The long-axis values were calculated from the X-ray diffraction patterns from crystals of all the LPSs in the low-angle region and they corresponded roughly to the length of the proposed primary chemical structures of the R cores of the LPSs. The volume occupied by a single molecule of all the LPSs were calculated from the molecular weights based on the proposed structures and the crystallographic data obtained by electron diffraction, X-ray diffraction, and density determination.

Crystallization↗
PubMed1991

Apolipoprotein (apo) E inhibits the capacity of monosodium urate crystals to stimulate neutrophils. Characterization of intraarticular apo E and demonstration of apo E binding to urate crystals in vivo.

Factors that modulate the ability of monosodium urate crystals to stimulate leukocytes could regulate gouty inflammation. Lipoproteins that bear apo B-100 and apo E bind to urate crystals and suppress crystal-neutrophil interaction. In this study, we observed that urate crystals, coated with apo E of monocyte origin, had a diminished ability to stimulate neutrophils. Apo E was also detected on the surface of urate crystals recovered from gout patients. Thus, we analyzed apo E in noninflammatory synovial fluid, and found it to be associated with particles of heterogeneous size and of predominantly alpha and pre-beta electrophoretic mobility. Local articular synthesis of at least a portion of synovial fluid apo E was suggested because (a) the synovial fluid/plasma concentration ratio of apo E was significantly higher than that for both apo B and apo A-I, which are not widely synthesized by extrahepatic tissues, (b) cultured rheumatoid synovial cells in first passage secreted apo E, (c) a portion of synovial fluid apo E was heavily sialylated. We conclude that synovial fluids contain apo E that appears partly of local origin. Apo E binds to urate crystals and could modulate gouty inflammation.

Apolipoproteins E↗
PubMedDate not supplied

Structural features of B-DNA dodecamer crystal structures: influence of crystal packing versus base sequence.

We have analyzed the set of inter and intra base pair parameters for each dinucleotide step in single crystal structures of dodecamers, solved at high and medium resolution and all crystallized in P2(1)2(1)2(1) space group. The objective was to identify whether all the structures which have either the Drew-Dickerson (DD) sequence d[CGCGAATTCGCG] with some base modification or related sequence (non-DD), would display the same sequence dependent structural variability about its palindromic sequence, despite the molecule being bent at one end because of similar crystal lattice packing effect. Most of the local doublet parameters for base pairs steps G2-C3 and G10-C11 positions, symmetrically situated about the lateral two-fold, were significantly correlated between themselves. In non-DD sequences, significant correlations between these positional parameters were absent. The different range of local step parameter values at each sequence position contributed to the gross feature of smooth helix axis bending in all structures. The base pair parameters in some of the positions, for medium resolution DD sequence, were quite unlike the high-resolution set and encompassed a higher range of values. Twist and slide are the two main parameters that show wider conformational range for the middle region of non-DD sequence structures in comparison to DD sequence structures. On the contrary, the minor and major groove features bear good resemblance between DD and non-DD sequence crystal structure datasets. The sugar-phosphate backbone torsion angles are similar in all structures, in sharp contrast to base pair parameter variation for high and low resolution DD and non-DD sequence structures, consisting of unusual (epsilon = g-, xi = t) BII conformation at the 10th position of the dodecamer sequence. Thus examining DD and non-DD sequence structures packed in the same crystal lattice arrangement, we infer that inter and intra base pair parameters are as symmetrically equivalent in its value as the symmetry related step for the palindromic DD sequence about lateral two-fold axis. This feature would lead us to agree with the conclusion that DNA conformation is not substantially affected by end-to-end or lateral inter-molecular interaction due to crystal lattice packing effect. Non-DD sequence structures acquire step parameter values which reflect the altered sequence at each of the dodecamer sequence position in the orthorhombic lattice while showing similar gross features of DD sequence structures.

Base Sequence↗
PubMed1999

Measurement of crystal thickness and crystal tilt from HRTEM images and a way to correct for their effects.

The effects of thickness and tilt angle are studied numerically on experimental high-resolution transmission electron microscope (HRTEM) images of a wedge-shaped metal oxide crystal. For sufficiently thin and well-aligned crystals, the amplitudes and phases of the Fourier transforms of the HRTEM images are essentially the same as the crystallographic structure factors. For tilted crystals, the changes of amplitudes and phases as a function of increased thickness and tilt angle can be described by a simple model. A method is presented by which the local thickness can be determined from one HRTEM image and one convergent-beam electron diffraction pattern from the same crystal. It is also shown how the projected potential can be reconstructed from HRTEM images of tilted crystals, disclosing the crystal structure, even from quite thick (>20 nm) samples.

Crystallography↗
PubMed1979

CLearance of calcium pyrophosphate dihydrate crystals in vivo. II. Studies using triclinic crystals doubly labeled with 45Ca and 85Sr.

The clearance rate of isotopically labeled synthetic triclinic calcium pyrophosphate dihydrate (CPPD) crystals injection into rabbit joints was estimated by serial counting. Kinetic analysis using a four compartment model showed that half of the injected dose was cleared from 4 rabbit knee joints in 19.1 +/- 0.42 (SEM) days. Profound hypomagnesemia, produced in 2 rabbits with a low magnesium diet, did not affect the rate of crystal clearance detectably. Lavage of joints with solutions known to promote CPPD crystal solubility failed to remove detectable radioactivity. The previous finding of CPPD crystals in synovial phagocytes by electron microscopy, together with the finding of nuclide activity in the synovium and the failure to remove such activity by joint lavage, suggests that endocytosis by synovial cells is an important, effective mechanism controlling the synovial fluid concentration of crystals in patients with CPPD crystal deposition disease.

Animals↗
PubMed2002

Hydration structure of human lysozyme investigated by molecular dynamics simulation and cryogenic X-ray crystal structure analyses: on the correlation between crystal water sites, solvent density, and solvent dipole.

The hydration structure of human lysozyme was studied with cryogenic X-ray diffraction experiment and molecular dynamics simulations. The crystal structure analysis at a resolution of 1.4 A provided 405 crystal water molecules around the enzyme. In the simulations at 300 K, the crystal structure was immersed in explicit water molecules. We examined correlations between crystal water sites and two physical quantities calculated from the 1-ns simulation trajectories: the solvent density reflecting the time-averaged distribution of water molecules, and the solvent dipole measuring the orientational ordering of water molecules around the enzyme. The local high solvent density sites were consistent with the crystal water sites, and better correlation was observed around surface residues with smaller conformational fluctuations during the simulations. Solvent dipoles around those sites exhibited coherent and persistent ordering, indicating that the hydration water molecules at the crystal water sites were highly oriented through the interactions with hydrophilic residues. Those water molecules restrained the orientational motions of adjoining water molecules and induced a solvent dipole field, which was persistent during the simulations around the enzyme. The coherent ordering was particularly prominent in and around the active site cleft of the enzyme. Because the ordering was significant up to the third to fourth solvent layer region from the enzyme surface, the coherently ordered solvent dipoles likely contributed to the molecular recognition of the enzyme in a long-distance range. The present work may provide a new approach combining computational and the experimental studies to understand protein hydration.

Chemical Phenomena↗
PubMed1985

Crystallization of phycoerythrocyanin from the cyanobacterium Mastigocladus laminosus and preliminary characterization of two crystal forms.

The light-harvesting protein phycoerythrocyanin from the cyanobacterium Mastigocladus laminosus Cohn has been crystallized in two different crystal forms by vapour diffusion. In 5% (w/v) polyethylene glycol at pH 8.5, hexagonal crystals of space group P63 with cell constants a = b = 158 A, c = 40.6 A were obtained, which turned out to be almost isomorphous with the hexagonal crystals of C-phycocyanin from the same organism. Consequently, the conformation of both phycobiliproteins must be very similar. From 1.5 M-ammonium sulfate (pH 8.5), orthorhombic crystals of space group P2221 with cell constants a = 60.5 A, b = 105 A, c = 188 A could be grown. Density measurements of these crystals indicate that the unit cell contains 18 (alpha beta)-units. A detailed packing scheme is proposed that is consistent with the observed pseudo-hexagonal X-ray intensity pattern and with the known size and shape of (alpha beta)3-trimers of C-phycocyanin. Accordingly, disc-like (alpha beta)3-trimers are associated face-to-face and stacked one upon another in rods with a period of 60.5 A, corresponding to the cell dimension a.

Crystallography↗
PubMed1987

Crystallization and preliminary analysis of crystals of cytochrome c2 from Rhodopseudomonas capsulata.

Two crystal forms of the cytochrome c2 isolated from Rhodopseudomonas capsulata have been obtained. One crystal form (type I), grown from ammonium sulfate solutions at pH 7.5, belongs to the space group R32 with unit cell dimensions of a = b = 100.0 A, and c = 162.2 A in the hexagonal setting. These crystals most likely contain two molecules in the asymmetric unit. The other crystal form (type II) was obtained from polyethylene glycol 6000 solutions at pH 6.5. Type II crystals belong to the space group P3(1)21 or P3(2)21 with one molecule per asymmetric unit and unit cell dimensions of a = b = 52.4 A, and c = 87.9 A. Both crystal forms diffract to at least 1.8 A resolution and appear to be resistant to radiation damage.

Crystallography↗