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PubMed1996

High-resolution structure (1.33 A) of a HEW lysozyme tetragonal crystal grown in the APCF apparatus. Data and structural comparison with a crystal grown under microgravity from SpaceHab-01 mission.

Crystals of tetragonal hen egg-white lysozyme were grown using Advanced Protein Crystallization Facility (APCF) apparatus under a microgravity environment (SpaceHab-01 mission) and ground control conditions. Crystals were grown from NaCl as a crystallizing agent at pH 4.3. The X-ray diffraction patterns of the best diffracting ground- and space-grown crystals were recorded using synchrotron radiation and an image plate on the W32 beamline at LURE. Both ground- and space-grown crystals showed nearly equivalent maximum resolution of 1.3-1.4 A. Refinements were carried out with the program X-PLOR with final R values of 18.45 and 18.27% for structures from ground- and space- grown crystals, respectively. The two structures are nearly identical with the root-mean-square difference on all protein atoms being 0.13 A. Some residues of the two refined structures show multiple alternative conformations. Two ions were localized into the electron-density maps of the two structures: one chloride ion at the interface between two symmetry-related molecules and one sodium ion stabilizing the loop Ser60-Leu75. The sodium ion is surrounded by six ligands which form a bipyramid around it at distances of 2.2-2.6 A.

Journal Article↗

PubMed1982

Enzymatic release of microspheroids containing hydroxyapatite crystals from synovium and of calcium pyrophosphate dihydrate crystals from cartilage.

Incubation of minced, focally calcified, chondromatosis tissue obtained at operation from a patient with Milwaukee shoulder (rotator cuff defect and glenohumeral osteoarthritis associated with synovial fluid, hydroxyapatite crystals in microspheroidal masses, collagenase, and neutral protease) with partially purified mammalian synovial cell collagenase released masses of hydroxyapatite crystals of the same size as those originally found in the patient's synovial fluid. Incubation of mineral articular cartilage obtained from a shoulder joint at arthroplasty for a destructive arthropathy in a patient with generalised calcium pyrophosphate dihydrate (CPPD) crystal deposition with partially purified synovial cell collagenase freed CPPD crystals from their matrix. These data are compatible with a previously postulated mechanism linking microcrystals to destructive arthropathies, that is, crystal endocytosis by synovial cells stimulating collagenase secretion with subsequent enzymatic crystal "strip-mining', releasing additional crystals into the synovial fluid in a self-perpetuating cycle.

Calcium Pyrophosphate↗

PubMed1991

Crystal-induced inflammation: studies of the mechanism of crystal-membrane interactions.

Studies of the interactions of monosodium urate monohydrate (MSUM) crystals and calcium pyrophosphate dihydrate triclinic (CPPD) crystals with biomembranes have been reviewed. Crystal-membrane binding and crystal-induced membranolysis have been studied using human erythrocytes as a model membrane system. The extent of MSUM-membrane binding was determined by incorporating a hydrophobic, fluorescent probe into the membranes, centrifugation to separate free membranes from membranes with bound crystals and quantitation of free membranes by measuring the total fluorescence intensity. The ability of MSUM and CPPD to hemolyse red cells was used as a measure of the membranolytic potential of the crystals. Fluorescence polarization studies showed that MSUM-membrane binding resulted in fluidization of the membrane. Cross-linking of the membrane proteins of the erythrocyte or the presence of divalent cations in the incubation medium inhibited MSUM induced hemolysis. These findings were explained by hypothesizing a "pore" model mechanism for MSUM induced membranolysis as follows. Binding of crystals to membranes induces the redistribution of transmembrane proteins into clusters or aggregates leading to "pore" formation. The "pores" permit the leakage of low molecular weight soluble compounds and ions acoss the membrane which is followed by osmotic rupture of the membrane.

Arthritis↗

PubMed1993

Observations of structural features and characteristics of biological apatite crystals. 3. Observation on ultrastructure of human dentin crystals.

In a series of studies to investigate the structural features of the biological crystals, using electron microscope, we examined the ultrastructure of the human dentin crystals at near atomic resolution through the cross and longitudinal sections of the crystals. The materials used for this study were the deep layer of the non-carious coronal dentin from freshly extracted human erupted permanent molars. The small cubes of the dentin were fixed in glutaraldehyde and osmium tetroxide and embedded in epoxy resin using the routine methods. The ultrathin sections were cut with a diamond knife without decalcification. The sections were examined with the HITACH H-700 type of transmission electron microscope operated at 200kV. Each crystal was observed at the initial magnification of 300,000 times and at the final magnification of 10,000,000 times and over. Using this approach, the authors have been able to show the configuration of the hydroxyapatite structure in the cross and longitudinal sections of the dentin crystals deposited within and between the collagen fibrils (intrafibrillar and interfibrillar crystal) in the intertubular dentin and observe the basic hexagonal pattern of the unit cell viewed down the c-axis. The authors sincerely believe that the electron micrograph shown in this report is the first atomic image to be obtained from a hydroxyapatite crystal from the human dentin, using the sections.

Apatites↗

PubMed1975

Succinylsulfathiazole crystal forms. III: Crystal growth studies.

Crystal growth accompanying the transformation of succinylsulfathiazole crystal forms in aqueous suspensions was studied using a projecting microscope. The effects of increase of temperature, agitation, inclusion of seeds of Form II (the water-stable dihydrate), sulfathiazole, methylcellulose, and polysorbate 80 on the particle-size distribution of anhydrous succinylsulfathiazole Form I were examined. Rates of crystal growth, calculated as increase of diameter per unit time, were given under different experimental conditions. Increase of temperature, agitation, and seeding with nuclei of Form II had significant growth-accelerating effects. Sulfathiazole and polysorbate 80 had growth-retarding effects. Methylcellulose inhibited the crystal growth of Form I for over a year. Aqueous suspensions of Form II did not show any change in particle-size distribution. The crystal growth was shown to be a direct consequence of the transformation of the crystal form. Physical conditions and additives which had accelerating or retarding effects on the rate of succinylsulfathiazole in aqueous suspensions.

Chemical Phenomena↗

PubMed1994

Comparison of the structures and the crystal contacts of trypanosomal triosephosphate isomerase in four different crystal forms.

Triosephosphate isomerase (TIM) is a dimeric enzyme consisting of 2 identical subunits. Trypanosomal TIM can be crystallized in 4 different spacegroups: P2(1)2(1)2(1), C2(big cell), C2(small cell), and P1. The P1 crystal form only grows in the presence of 1.4 M DMSO; there are 2 DMSO binding sites per subunit. The structures have been refined at a resolution of 1.83 A, 2.10 A, 2.13 A, and 1.80 A, respectively. In the 4 different spacegroups the TIM subunit can be observed in the context of 7 different crystallographic environments. In the C2 cells, the dimer 2-fold axis coincides with a crystallographic 2-fold axis. The similarities and differences of the 7 subunits are discussed. In 6 subunits the flexible loop (loop 6) is open, whereas in the P2(1)2(1)2(1) cell, the flexible loop of subunit 2 is in an almost closed conformation. The crystal contacts in the 4 different crystal forms are predominantly generated by polar residues in loops. A statistical analysis of the residues involved in crystal contacts shows that, in particular, serines are frequently involved in these interactions; 19% of the exposed serines are involved in crystal contacts.

Amino Acid Sequence↗

PubMed1994

Crystallization and molecular packing analysis of barstar crystals.

Barstar, the natural inhibitor of barnase crystallizes in many different crystal forms under almost identical conditions. Although barstar is a monomeric protein, it crystallizes with four molecules in the asymmetric unit in two crystal forms, rhombohedral (space group R3; a = b = 118.0 angstrum; c = 75.5 angstrum) and tetragonal (space group P4; a = b = 105.1 angstrum; c = 36.0 angstrum), which exist simultaneously under identical crystallization conditions. The relation between the four molecules in the asymmetric unit of the crystals belonging to space group P4 can be interpreted in terms of a small distortion in the crystallographic symmetry of the higher symmetry space group P422.

Bacterial Proteins↗

PubMed2002

Bicelle crystallization: a new method for crystallizing membrane proteins yields a monomeric bacteriorhodopsin structure.

Obtaining crystals of membrane proteins that diffract to high resolution remains a major stumbling block in structure determination. Here we present a new method for crystallizing membrane proteins from a bicelle forming lipid/detergent mixture. The method is flexible and simple to use. As a test case, bacteriorhodopsin (bR) from Halobacterium salinarum was crystallized from a bicellar solution, yielding a new bR crystal form. The crystals belong to space group P2(1) with unit cell dimensions of a=45.0 A, b=108.9 A, c=55.9 A, beta=113.58 degrees and a dimeric asymmetric unit. The structure was solved by molecular replacement and refined at 2.0 A resolution. In all previous bR structures the protein is organized as a parallel trimer, but in the crystals grown from bicelles, the individual bR subunits are arranged in an antiparallel fashion.

Bacteriorhodopsins↗

PubMed1998

Lysozyme crystal growth, as observed by small angle X-ray scattering, proceeds without crystallization intermediates.

A combination of small angle X-ray scattering and gel techniques was used to follow the kinetics of protein crystal growth as a function of time. Hen egg white lysozyme, at different protein concentrations, was used as a model system. A new sample holder was designed, in which supersaturation is induced in the presence of salt by decreasing the temperature. It had been shown previously that a decrease in temperature and/or an increase in crystallizing agent induces an increase in the attractive interactions present in the lysozyme solutions, the lysozyme remaining monomeric. In the present paper we show that similar behaviour is observed in NaCl when agarose gels are used. During crystal growth, special attention was paid to determine whether oligomers were formed as the protein in solution was incorporated in the newly formed crystals. From these first series of experiments, we did not find any indication of oligomer formation between monomer in solution and crystal. The results obtained are in agreement with the hypothesis that lysozyme crystals in NaCl grow by addition of monomeric particles.

Crystallization↗

PubMed2003

Molecular crystals: the crystal field effect on molecular electronic structure.

The effect of crystal packing on the electronic structure of organic molecules was modeled by incorporation of the external electrostatic potential into the semiempirical Hamiltonian of the molecule. An empirical correction procedure was devised in order to compensate for systematic errors in the charge distribution typical of semiempirical methods. The model was applied to 79 crystal structures belonging to various syngonies and space groups. The effect of the crystal field is subject to wide variations depending on the crystal packing motif. The difference between the effect of the crystal field on the molecular electronic structure and the solvent effect modeled with COSMO is highlighted. The effect of intermolecular hydrogen bonds on the molecular electronic structure and electronic spectra was modeled with this approach, and it does not predominate over the effect of long-range electrostatic interactions. INDO/S calculations employing the crystal electrostatic potential give an insight into the origin of crystallochromy, in particular, they properly predict color difference for several groups of polymorphs.

Algorithms↗

PubMed2005

Spectroscopic imaging of protein crystals in crystallization drops.

Automatic imaging and scoring of crystallization drops is an essential step in high-throughput crystallography. Presently, white-light images of crystallization drops are acquired robotically and the images are analyzed and scored using pattern recognition algorithms. However, the scoring part remains unreliable as crystals and microcrystals are not always recognized by existing feature-extraction and recognition algorithms. We propose a fundamental shift in crystal monitoring through spectroscopic imaging of crystallization drops. This method converts the problem of automatic crystal detection from one of pattern recognition into one of intensity (concentration) analysis. The latter can be more robust and reliable.

Crystallization↗

PubMed1999

Crystallization of the immunodominant outer membrane protein OmpC; the first protein crystals from Salmonella typhi, a human pathogen.

OmpC, a surface antigen of Salmonella typhi was crystallized after several attempts, using PEG 3350. Well shaped hexagonal crystals were grown from vapor diffusion method using octyl glucoside and C12E9 as detergents. Crystals are sensitive to X-ray and diffract weakly up to 7 A. Porin isoforms, due to the bound lipopolysaccharides, could be the cause for poor diffraction. Crystal quality depends largely on the purification method, and in case of LPS contamination, the genetic background of the bacteria. Crystallization and initial data collection suggest optimum conditions and the method of choice for OmpC crystallization.

Antigens, Bacterial↗

PubMed1986

Modifiers of calcium oxalate crystallization found in urine. I. Studies with a continuous crystallizer using an artificial urine.

Various modifiers of the rate of crystallization of calcium oxalate (CaOx) known to be present in urine were studied in a continuous crystallizer system under conditions approximating those in whole urine. Of the small ions examined, magnesium and citrate were only weak inhibitors of the crystal growth rate and degree of agglomeration of CaOx within the urinary range of concentration of these ions. At and beyond the upper limit of the normal, however, both ions became much more active mainly through their ability to complex oxalate and calcium ions respectively. Pyrophosphate showed similar characteristics although its ability to act as an inhibitor at high concentrations was not due to complexation of calcium ions but to adsorption onto the crystal surface of the freshly generated CaOx crystals. The polyanionic inhibitors, chondroitin-4-sulphate, heparin and ribonucleic acid (RNA), also acted as adsorption inhibitors of growth and agglomeration. Of all the inhibitors tested RNA was the most active within the concentration range found in normal urine. Under the conditions of ionic strength employed, it was not possible to measure the effect of Tamm-Horsfall mucoprotein satisfactorily since it polymerized to form particles sufficiently large to interfere with the true crystal counts of CaOx in the test system.

Calcium Oxalate↗

PubMed1981

Molecular complex of lumiflavin and 2-aminobenzoic acid: crystal structure, crystal spectra, and solution properties.

The molecular complex lumiflavin-2-aminobenzoic acid monohydrate (C13H12N4O2.C7H7NO2.H2O) crystallizes from from aqueous solution as red triclinic prisms. The space group is P1 with cell dimensions a = 9.660 A, b = 14.866 A, c = 7.045 A, alpha = 95.44 degrees , beta = 95.86 degrees, and gamma = 105.66 degrees . The crystal structure was solved by direct methods and refined by block-diagonal least-squares procedures to an R value of 0.050 on the basis of 1338 observed reflections. The structure is composed of stacks of alternating lumiflavin adn un-ionized (neutral) 2-aminobenzoic acid molecules. Two different modes of stacking interaction are observed. In one, 2-aminobenzoic acid overlaps all three of the isoalloxazine rings, at a mean distance of 3.36 A; in the other, 2-aminobenzoic acid interacts distance of 3.36 A; in the other, 2-aminobenzoic acid interacts with the pyrazine and dimethylbenzene moieties, at a distance of 3.42 A. Perpendicular to the stacking direction, the molecules form a continuous sheet. Each flavin is hydrogen bonded via O(2) and NH(3) to two symmetrically related aminobenzoates; the water of crystallization forms three hydrogen bonds, bridging two flavins, via O(4) and N(5), and one aminobenzoic acid. The red color of the crystals results from a charge-transfer transition involving stacked flavin and 2-aminobenzoic acid. The red color of the crystals results from a charge-transfer transition involving stacked flavin and 2-aminobenzoic acid molecules. Measurements of the polarized optical absorption spectra of crystals show that the transition moment direction for the long wavelength absorbance (beyond 530 nm) contains an out-of-plane component which can only arise from a charge-transfer interaction. Since the amino N does not make exceptionally close interactions with isoalloxazine atoms in either stacking mode (minimum interatomic distance 3.52 A), the charge transfer is presumed to involve pi orbitals of the 2-aminobenzoic acid donor.

Chemical Phenomena↗

PubMed2006

From surface self-assembly to crystallization: prediction of protein crystallization conditions.

A new criterion based on surface and volume diffusion kinetics was established to predict protein crystallization. Similar to the layer-by-layer crystal growth process of protein, the kinetics of the two-dimensional self-assembly of protein at the aqueous solution surface provides a convenient and reliable way to estimate the surface integration and the volume transport during protein crystallization. Both the surface and diffusion kinetics were estimated based on the protein self-assembly at the air/solution interface, which can be obtained by measuring the surface tension. A crystallization coefficient is found to provide an effective and reliable criterion to predict protein crystallization conditions. This criterion has been applied to lysozyme, concanavalin A and BSA crystallization, and it turns out to be very successful and more reliable than the second virial coefficient criterion.

Animals↗

PubMed1997

Glycosaminoglycans in crystal-surface binding substances and their role in calcium oxalate crystal growth.

OBJECTIVE: To clarify the role of glycosaminoglycans (GAGs) in crystal-surface binding substances (CSBS) on the growth of calcium oxalate crystals in urine. MATERIALS AND METHODS: Urine samples (24 h) were collected from healthy men (aged 25-42 years) and CSBS were obtained from the pooled urine samples. The CSBS were digested with heparitinase or proteinase and the inhibition of crystal growth assessed before and after enzyme digestion. Anion-exchange chromatography and high-performance liquid chromatography (HPLC) were used to determine the types of GAGs contained in the CSBS. RESULTS: The inhibitory activity of CSBS on crystal growth decreased with concentration when digested with heparitinase or proteinase. HPLC showed that CSBS contained a small amount of dermatan sulphate and abundant heparan sulphate, both of which inhibited crystal growth. CONCLUSION: Both heparan sulphate and dermatan sulphate may inhibit calcium oxalate crystallization, the former being the predominant GAG in CSBS.

Adult↗

PubMed2006

Production and basic morphology of struvite crystals from a pilot-scale crystallization process.

A pilot-scale, struvite crystallization process was operated using anaerobic digester supernatants from two, full-scale, treatment plants as influent. It was found that the produced struvite crystals were easily separated from the process and were composed of very pure struvite (91.2 % to 94.1 % purity), with small amounts of calcium and carbonate, and traces of iron and aluminum. Most of the harvested struvite crystals, which were an aggregation of numerous fine crystals, were round, hard and larger than 1.5 mm in mean diameter. The crystal retention time in the reactor and the magnesium dosage in the supernatant appeared to have a significant effect on the crystal size, hardness and morphology.

Crystallization↗

PubMed2000

Local conformational variations observed in B-DNA crystals do not improve base stacking: computational analysis of base stacking in a d(CATGGGCCCATG)(2) B<-->A intermediate crystal structure.

The crystal structure of d(CATGGGCCCATG)(2) shows unique stacking patterns of a stable B<-->A-DNA intermediate. We evaluated intrinsic base stacking energies in this crystal structure using an ab initio quantum mechanical method. We found that all crystal base pair steps have stacking energies close to their values in the standard and crystal B-DNA geometries. Thus, naturally occurring stacking geometries were essentially isoenergetic while individual base pair steps differed substantially in the balance of intra-strand and inter-strand stacking terms. Also, relative dispersion, electrostatic and polarization contributions to the stability of different base pair steps were very sensitive to base composition and sequence context. A large stacking flexibility is most apparent for the CpA step, while the GpG step is characterized by weak intra-strand stacking. Hydration effects were estimated using the Langevin dipoles solvation model. These calculations showed that an aqueous environment efficiently compensates for electrostatic stacking contributions. Finally, we have carried out explicit solvent molecular dynamics simulation of the d(CATGGGCCCATG)(2) duplex in water. Here the DNA conformation did not retain the initial crystal geometry, but moved from the B<-->A intermediate towards the B-DNA structure. The base stacking energy improved in the course of this simulation. Our findings indicate that intrinsic base stacking interactions are not sufficient to stabilize the local conformational variations in crystals.

Base Composition↗