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Surface chemistry of enamel apatite during maturation in relation to pH: implications for protein removal and crystal growth.

Apatite crystal growth rate and morphology in mineralized tissues are considered to be controlled by surface interaction with extracellular matrix proteins. During enamel maturation where protein is finally removed from crystal surfaces to permit massive crystal growth, pH oscillates between approximately 5.8 and approximately 7.2. With this in mind, a study of enamel apatite surface chemistry in terms of local environmental pH was undertaken. Using atomic force microscopy adhesion force measurements were made between hydroxylated or carboxylated cantilever tips and maturation stage crystals between pH 2 and 10. Adhesion force increased from pH 10 to a maximum at pH 6.6 presumably due to increased hydrogen bonding due to replacement of surface cations (Na, Ca, Mg) with protons and/or protonation of phosphate per se. Below pH 6.6 adhesion force decreased and became very variable indicating that the surface had become unstable probably due to removal of fully protonated phosphate from the surface by adherence to the cantilever tip. Frictional force measurements also revealed 2-3, approximately 30 nm diameter high friction domains in bands across the crystal long axis. Their location mirrored the binding pattern of similarly sized amelogenin aggregates seen in vitro. The data suggests that specific protein binding sites may exist on crystal surfaces and may be released at lower pH by protonation which would lower cationic charge on both crystal surface and ionic charge on the protein. Instability of the crystal surface could also play a role.

Animals↗

Detection and characterization of merohedral twinning in crystals of oxalyl-coenzyme A decarboxylase from Oxalobacter formigenes.

Oxalyl-coenzyme A decarboxylase is a thiamin diphosphate dependent enzyme active in the catabolism of the highly toxic compound oxalate. The enzyme from Oxalobacter formigenes has been expressed as a recombinant protein in Escherichia coli, purified to homogeneity and crystallized. Two crystal forms were obtained, one showing poor diffraction and the other merohedral twinning. Crystals in the former category belong to the tetragonal space group P4(2)2(1)2. Data to 4.1 A resolution were collected from these crystals and an incomplete low resolution structure was initially determined by molecular replacement. Crystals in the latter category were obtained by co-crystallizing the protein with coenzyme A, thiamin diphosphate and Mg(2+)-ions. Data to 1.73 A were collected from one of these crystals with apparent point group 622. The crystal was found to be heavily twinned, and a twin ratio of 0.43 was estimated consistently by different established methods. The true space group P3(1)21 was deduced, and a molecular replacement solution was obtained using the low resolution structure as template when searching in detwinned data.

Carboxy-Lyases↗

Crystallization and X-ray diffraction of spray-dried and freeze-dried amorphous lactose.

Crystallization of spray-dried and freeze-dried amorphous lactose over different relative vapor pressures (RVP) and storage times was studied. Crystallization was observed from increasing peak intensities in X-ray diffraction patterns. Lactose was crystallized in the samples stored at RVP of 44.1% and above in both types of dehydrated powders. The rate of crystallization increased with increasing RVP and storage time. Similar crystallization behavior of both spray-dried and freeze-dried lactose was observed. Lactose crystallized as alpha-lactose monohydrate, anhydrous beta-lactose, and the anhydrous form of alpha- and beta-lactose in a molar ratio of 5:3 and 4:1 in both spray-dried and freeze-dried forms. Peak intensities of X-ray diffraction patterns for anhydrous beta-lactose were decreased, and for alpha-lactose monohydrate increased with increasing storage RVP and time. The crystallization data were successfully modeled using Avrami equation at RVP of 54.5% and above. The crystallization data obtained is helpful in understanding and predicting storage stability of lactose-containing food and pharmaceutical products.

Crystallization↗

Effects of escin on indinavir crystallization time in the urine of patients with HIV-I infection: a multicenter, randomized, open-label, controlled, four-period crossover trial.

BACKGROUND: The combination of indinavir, a protease inhibitor, and reverse-transcriptase inhibitors is widely used in the treatment of HIV-1 infection. However, precipitation of indinavir crystals in the renal tubular lumen due to the drug's aqueous insolubility may result in characteristic symptoms of flank pain or classic renal colic. An in vitro study has shown that addition of escin to synthetic urine containing indinavir delayed the crystallization time of indinavir. OBJECTIVE: This study examined the efficacy and tolerability of the addition of escin to highly active antiretroviral therapy containing indinavir to delay the crystallization time of indinavir in urine. METHODS: This was a multicenter, randomized, open-label, controlled, 4-period crossover trial in which each period lasted 4 weeks. HIV-1-infected adults receiving treatment with indinavir plus 2 nucleoside analogue reverse-transcriptase inhibitors in whom plasma viral loads had been undetectable (HIV-1 RNA <200 copies/mL) for at least 6 months were randomly assigned to 1 of 2 groups based on the timing of the initiation of escin. Group I received escin during the second and third treatment periods, and group II received escin during the first and fourth treatment periods. The primary end point was the in vitro crystallization time of indinavir in 24-hour urine specimens, determined at the end of each 4-week period. Tolerability was assessed based on the number of patients with a rebound in plasma viral load and on the numbers of clinically and biologically relevant adverse events (including those requiring discontinuation of treatment). Clinical and laboratory evaluations were performed throughout each 4-week period. RESULTS: Fifty HIV-1-infected patients were enrolled, 47 were randomized to treatment (40 [85.1%] men, 7 [14.9%] women; median [interquartile range] age, 36 [34-45] years), and 30 completed the study. Urine pH and plasma and urine indinavir concentrations were unaffected by the addition of escin to antiretroviral treatment. The mean time to the onset of crystallization was 14.7 minutes with escin (95% Cl, 11.8-17.5) and 9.9 minutes without it (95% Cl, 6.7-13.1). Therefore, the addition of escin increased the mean crystallization time by 5.5 minutes (95% Cl, 1.5-9.5; P = 0.008), representing the overall capacity of study treatment to inhibit indinavir crystallization in the urine. Three of 47 patients had mild gastrointestinal symptoms associated with escin treatment. No episodes of nephrolithiasis were recorded during the study or after the completion of study treatment. CONCLUSION: The results of this prospective clinical trial of the effect of escin on indinavir crystallization time support the possibility that indinavir-associated nephrolithiasis may be prevented by means other than overhydration. Further research is needed in greater numbers of patients over longer follow-up times.

Adult↗

Crystallization of oxytetracycline from fermentation waste liquor: influence of biopolymer impurities.

Organic impurities in the fermentation broth of antibiotic production impose great difficulties in the crystallization and recovery of antibiotics from the concentrated waste liquor. In the present laboratory study, the inhibitory effect of biopolymers on antibiotic crystallization was investigated using oxytetracycline (OTC) as the model antibiotic. Organic impurities separated from actual OTC fermentation waste liquor by ultrafiltration were dosed into a pure OTC solution at various concentrations. The results demonstrated that small organic molecules with an apparent molecular weight (AMW) of below 10,000 Da did not affect OTC crystallization significantly. However, large biopolymers, especially polysaccharides, in the fermentation waste caused severe retardation of crystal growth and considerable deterioration in the purity of the OTC crystallized. Atomic force microscopy (AFM) revealed that OTC nuclei formed in the solution attached to the surfaces of large organic molecules, probably polysaccharides, instead of being surrounded by proteins as previously thought. It is proposed that the attachment of OTC nuclei to biopolymers would prevent OTC from rapid crystallization, resulting in a high OTC residue in the aqueous phase. In addition, the adsorption of OTC clusters onto biopolymers would destabilize the colloidal system of organic macromolecules and promote particle flocculation. OTC crystallization would therefore take place with the precipitation of abundant organic impurities. Hence, the removal of polysaccharides and other biopolymers by ultrafiltration can be an effective means of improving the recovery of OTC and similar antibiotics by crystallization from the fermentation waste.

Biopolymers↗

Crystal structures of the signal transducing protein GlnK from Thermus thermophilus HB8.

The Thermus thermophilus HB8 genome encodes a signal transducing PII protein, GlnK. The crystal structures of GlnK have been determined in two different space groups, P2(1)2(1)2(1) and P3(1)21. The PII protein has the T-loop, which is essential for interactions with receptor proteins. In both crystal forms, three GlnK molecules form a trimer in the asymmetric unit. In one P2(1)2(1)2(1) crystal form, the three T-loops in the trimer are disordered, while in another P2(1)2(1)2(1) crystal form, the T-loop from one molecule in the trimer is ordered. In the P3(1)21 crystal, one T-loop is ordered while the other two T-loops are disordered. The conformations of the ordered T-loops significantly differ between the two crystal forms; one makes the alpha-helix in the middle of the T-loop, while the other has an extension of the beta-hairpin. Two different conformations are captured by the crystal contacts. The observation of multiple T-loop conformations suggests that the T-loop could potentially exhibit "polysterism," which would be important for interactions with receptor proteins. The crystal structures of the nucleotide-bound forms, GlnK.ATP and GlnK.ADP, have also been determined. ATP/ADP binding within a cleft at the interface of two adjacent T. thermophilus GlnK monomers might affect the conformation of the T-loop.

Adenosine Diphosphate↗

The effect of recombinant mouse amelogenins on the formation and organization of hydroxyapatite crystals in vitro.

Amelogenin is the most abundant protein in developing dental enamel. It is believed to play an important role in the regulation of the growth and organization of enamel crystals. Amelogenin, unlike many other proteins found in biominerals, is mostly hydrophobic except for a 13 amino acid hydrophilic C-terminal domain. To clarify the role of amelogenin in enamel mineralization, we designed calcium phosphate crystal growth experiments in the presence of recombinant amelogenins with or without the charged C-terminal domain. The shape and organization of the crystals were examined by TEM in bright field and diffraction modes. It was found that both full-length and truncated amelogenin inhibit crystal growth in directions normal to the c-axis. At the same time, crystallites organized into parallel arrays only in the presence of the full-length amelogenin in monomeric form. Pre-assembled amelogenins had no effect on crystals organization. These results imply that the hydrophobic portion of amelogenin plays a role in an inhibition of crystal growth, whereas the C-terminal domain is essential for the alignment of crystals into parallel arrays. Our data also suggest that nascent enamel structure emerges as a result of cooperative interactions between forming crystals and assembling proteins.

Amelogenin↗

Purification, crystallization, and properties of F1-ATPase complexes from the thermoalkaliphilic Bacillus sp. strain TA2.A1.

Recently, we reported the cloning of the atp operon encoding for the F(1)F(0)-ATP synthase from the extremely thermoalkaliphilic bacterium Bacillus sp. strain TA2.A1. In this study, the genes encoding the F(1) moiety of the enzyme complex were cloned from the atp operon into the vector pTrc99A and expressed in Escherichia coli in two variant complexes, F(1)-wt consisting of subunits alpha(3)beta(3)gammadeltaepsilon and F(1)Deltadelta lacking the entire delta-subunit as a prerequisite for overproduction and crystallization trials. Both F(1)-wt and F(1)Deltadelta were successfully overproduced in E. coli and purified in high yield and purity. F(1)Deltadelta was crystallized by micro-batch screening yielding three-dimensional crystals that diffracted to a resolution of 3.1A using a synchrotron radiation source. After establishing cryo and dehydrating conditions, a complete set of diffraction data was collected from a single crystal. No crystals were obtained with F(1)-wt. Data processing of diffraction patterns showed that F(1)Deltadelta crystals belong to the orthorhombic space group P2(1)2(1)2(1) with unit cell parameters of a=121.70, b=174.80, and c=223.50A, alpha, beta, gamma=90.000. The asymmetric unit contained one molecule of bacterial F(1)Deltadelta with a corresponding volume per protein weight (V(M)) of 3.25A(3) Da(-1) and a solvent content of 62.1%. Silver staining of single crystals of F(1)Deltadelta analyzed by SDS-PAGE revealed four bands alpha, beta, gamma, and epsilon with identical M(r)-values as those found in the native F(1)F(0)-ATP synthase isolated from strain TA2.A1 membranes. ATPase assays of F(1)Deltadelta crystals exhibited latent ATP hydrolytic activity that was highly stimulated by lauryldimethylamine oxide, a hallmark of the native enzyme.

Bacillus↗

Membrane-protein stability in a phospholipid-based crystallization medium.

Protein stability is a crucial factor to consider when attempting to crystallize integral membrane proteins. Cubic phase, or in meso, lipid-bilayer crystallization media are thought to provide native-like environments that should facilitate membrane protein crystallization by helping to stabilize the native protein conformation for the duration of the crystallization process. While excellent crystals of bacteriorhodopsin (bR) and other Halobacterial rhodopsins have been obtained in lipid-bilayer gels formed with monoglycerides, success remains elusive in the general application of such media to other membrane proteins. Additionally, we have noted that some mutants of bR are highly unstable in gels formed with monoolein. Phosphatidylethanolamines (PE) and derivatives of PE represent another class of lipids that can form connected-bilayer gels. When wildtype bR and a labile bR mutant were reconstituted into this phospholipid gel, spectroscopy showed that the protein is both more stable and has improved conformational homogeneity as compared to gels formed using monoolein. In addition, we demonstrate that well-diffracting crystals of bR can be grown from a PE-based crystallization medium. Since most proteins lack a stability-indicating chromophore and other structure-based analytical techniques are poorly compatible with the lipid gel, we developed a generally-applicable spectroscopic technique based on the intrinsic fluorescence of tryptophan residues. This fluorescence assay makes possible the rapid evaluation of lipid gels as media for the crystallization of membrane proteins.

Bacterial Proteins↗

Growth and disorder of macromolecular crystals: insights from atomic force microscopy and X-ray diffraction studies.

The growth processes and defect structures of protein and virus crystals have been studied in situ by atomic force microscopy (AFM), X-ray diffraction topography, and high-resolution reciprocal space scanning. Molecular mechanisms of macromolecular crystallization were visualized and fundamental kinetic and thermodynamic parameters, which govern the crystallization process of a number of macromolecular crystals, have been determined. High-resolution AFM imaging of crystal surfaces provides information on the packing of macromolecules within the unit cell and on the structure of large macromolecular assemblies. X-ray diffraction techniques provide a bulk probe with poorer spatial resolution but excellent sensitivity to mosaicity and strain. Defect structures and disorder created in macromolecular crystals during growth, seeding, and post-growth treatments including flash cooling were characterized and their impacts on the diffraction properties of macromolecular crystals have been analyzed. The diverse and dramatic effects of impurities on growth and defect formation have also been studied. Practical implications of these fundamental insights into the improvement of macromolecular crystallization protocols are discussed.

Chemistry Techniques, Analytical↗

Predictive models for protein crystallization.

Crystallization of proteins is a nontrivial task, and despite the substantial efforts in robotic automation, crystallization screening is still largely based on trial-and-error sampling of a limited subset of suitable reagents and experimental parameters. Funding of high throughput crystallography pilot projects through the NIH Protein Structure Initiative provides the opportunity to collect crystallization data in a comprehensive and statistically valid form. Data mining and machine learning algorithms thus have the potential to deliver predictive models for protein crystallization. However, the underlying complex physical reality of crystallization, combined with a generally ill-defined and sparsely populated sampling space, and inconsistent scoring and annotation make the development of predictive models non-trivial. We discuss the conceptual problems, and review strengths and limitations of current approaches towards crystallization prediction, emphasizing the importance of comprehensive and valid sampling protocols. In view of limited overlap in techniques and sampling parameters between the publicly funded high throughput crystallography initiatives, exchange of information and standardization should be encouraged, aiming to effectively integrate data mining and machine learning efforts into a comprehensive predictive framework for protein crystallization. Similar experimental design and knowledge discovery strategies should be applied to valid analysis and prediction of protein expression, solubilization, and purification, as well as crystal handling and cryo-protection.

Bayes Theorem↗

Two-dimensional crystallization of Ca-ATPase by detergent removal.

By using Bio-Beads as a detergent-removing agent, it has been possible to produce detergent-depleted two-dimensional crystals of purified Ca-ATPase. The crystallinity and morphology of these different crystals were analyzed by electron microscopy under different experimental conditions. A lipid-to-protein ratio below 0.4 w/w was required for crystal formation. The rate of detergent removal critically affected crystal morphology, and large multilamellar crystalline sheets or wide unilamellar tubes were generated upon slow or fast detergent removal, respectively. Electron crystallographic analysis indicated unit cell parameters of a = 159 A, b = 54 A, and gamma = 90 degrees for both types of crystals, and projection maps at 15-A resolution were consistent with Ca-ATPase molecules alternately facing the two sides of the membrane. Crystal formation was also affected by the protein conformation. Indeed, tubular and multilamellar crystals both required the presence of Ca2+; the presence of ADP gave rise to another type of packing within the unit cell (a = 86 A, b = 77 A, and gamma = 90 degrees), while maintaining a bipolar orientation of the molecules within the bilayer. All of the results are discussed in terms of nucleation and crystal growth, and a model of crystallogenesis is proposed that may be generally true for asymmetrical proteins with a large hydrophilic cytoplasmic domain.

Animals↗

Effects of ethyleneglycol chain length of dodecyl polyethyleneglycol monoether on the crystallization of bovine heart cytochrome c oxidase.

Tetragonal crystals that diffracted X-rays up to 5 A resolution were obtained from bovine heart cytochrome c oxidase isolated and solubilized with dodecyl octaethyleneglycol monoether, CH3(CH2)11O(CH2CH2O)8H. Comparison of observed structure factors between data sets each obtained from a different native crystal gave correlation coefficients of 0.92, 0.84 and 0.57 at 10 A, 7 A and 6 A resolution, respectively. The space group and the cell dimensions of the crystal are I4(1) or I4(3) and a = b = 253 A, c = 507 A, respectively. The perfection and stability of the tetragonal crystals are significantly higher than those of the hexagonal crystals of the protein stabilized with Brij-35, CH3(CH2)11O(CH2CH2O)23H (whose details are reported elsewhere). Examination of the effect of ethyleneglycol chain length on the crystallization revealed that only dodecyl polyethyleneglycol monoethers with eight and seven units were appropriate for producing this type of crystal, indicating an optimum size of the detergent for crystallization of the membrane protein.

Animals↗

A new approach to the study of urinary macromolecules as a participant in calcium oxalate crystallization.

Despite intense investigation, the relationship of urinary proteins to urinary stone matrix formation remains poorly understood. In an attempt to gain more information regarding this interaction, the binding of urinary proteins to calcium oxalate crystals formed in urine in vitro was studied. 0.1 M calcium chloride and 0.1 M sodium oxalate were added to an aliquot of urine collected from five non-infected, non-stone forming males. The resulting calcium oxalate crystals were centrifuged and the pellet demineralized with 5% EDTA. Gel filtration chromatography was used to isolate the protein fraction from the urine samples before and after crystallization of calcium oxalate. The proteins recovered from the crystals and urine were separated by two-dimensional polyacrylamide gel electrophoresis. Many, but not all of the urinary proteins were bound by the crystals. Albumin, seen to the most abundant urinary protein, was absent or markedly diminished in all instances, and the second most abundant urinary protein, PC-30, became the predominant protein component of the crystals. An unidentified protein with approximate molecular weight of 22,000 daltons and isoelectric point of 6.4 was highly concentrated by the crystals even when undetected in the urine. The study suggests that the binding of urinary proteins to calcium oxalate crystals formed in urine in vitro is not a random event but rather a selective phenomenon.

Adult↗

Strong inhibition of crystal-cell attachment by pediatric urinary macromolecules: a close relationship with high urinary citrate secretion.

OBJECTIVES: To investigate other reasons for the low incidence of pediatric urolithiasis, we evaluated the difference in the crystal-cell adhesion inhibitory activity of urinary macromolecules (UMMs) between children and adults. We also evaluated whether citrates influence the above inhibitory activity, because citrates are important in pediatric urine. METHODS: Urine samples were collected from children and healthy male adults during a 24-hour period, and urinary components with a molecular weight of 3 kDa or greater were extracted as UMMs to compare their inhibitory activity during the adhesion of calcium oxalate monohydrate crystals to cultured Madin-Darby canine kidney cells between children and adults. Subsequently, various concentrations of citrates were added to adult UMMs to evaluate the changes in the crystal-cell adhesion inhibitory activity of UMMs. RESULTS: Pediatric UMMs more strongly inhibited the adhesion of calcium oxalate monohydrate crystals to cultured Madin-Darby canine kidney cells at a concentration of 0.1 mg/mL compared with adult UMMs. In addition, pediatric UMMs contained higher proportions of fibronectin and glycosaminoglycans, both of which exhibit crystal-cell adhesion inhibitory activity. When citrates were added to adult UMMs, the crystal-cell adhesion inhibitory activity of UMMs was increased in a dose-dependent manner. However, citrates alone did not result in any differences in the inhibitory activity at any of the three different concentrations. CONCLUSIONS: We speculate that the incidence of pediatric urolithiasis is low because pediatric UMMs more potently inhibit the adhesion of calcium oxalate crystals to renal tubular cells or because the higher proportion of citrates in pediatric urine enhances the crystal-cell adhesion inhibitory activity of UMMs in a dose-dependent manner.

Adult↗

Protein crystallization under high pressure.

Pressure is expected to be an important parameter to control protein crystallization, since hydrostatic pressure affects the whole system uniformly and can be changed very rapidly. So far, a lot of studies on protein crystallization have been done. Solubility of protein depends on pressure. For instance, the solubility of tetragonal lysozyme crystal increased with increasing pressure, while that of orthorhombic crystal decreased. The solubility of subtilisin increased with increasing pressure. Crystal growth rates of protein also depend on pressure. The growth rate of glucose isomerase was significantly enhanced with increasing pressure. The growth rate of tetragonal lysozyme crystal and subtilisin decreased with increasing pressure. To study the effects of pressure on the crystallization more precisely and systematically, hen egg white lysozyme is the most suitable protein at this stage, since a lot of data can be used. We focused on growth kinetics under high pressure, since extensive studies on growth kinetics have already been done at atmospheric pressure, and almost all of them have explained the growth mechanisms well. The growth rates of tetragonal lysozyme decreased with pressure under the same supersaturation. This means that the surface growth kinetics significantly depends on pressure. By analyzing the dependence of supersaturation on growth rate, it was found that the increase in average ledge surface energy of the two-dimensional nuclei with pressure explained the decrease in growth rate. At this stage, it is not clear whether the increase in surface energy with increasing pressure is the main reason or not. Fundamental studies on protein crystallization under high pressure will be useful for high pressure crystallography and high pressure protein science.

Animals↗

Ibuprofen crystals with optimized properties.

The common analgesic drug ibuprofen shows bad dissolution and tableting behavior due to its hydrophobic structure. Additionally its high cohaesivity results in low flowability. Because of the bad compaction behavior ibuprofen has to be granulated usually before tableting. Another problem in manufacturing is the high tendency for sticking to the punches. A crystal form with optimized properties of ibuprofen was prepared and characterized in this study. Crystallization was carried out using the solvent change technique in the presence of different water-soluble additives. These additives were only present during the crystallization process and removed after precipitation by a washing process. A nearly pure ibuprofen powder was received, as GC-analysis showed. Plate-shaped crystals with increased powder dissolution, increased flowability and good tableting behavior were obtained. All crystals were determined as isomorphic by DSC and X-ray analysis. Thus the improvement of the substance characteristics of ibuprofen is reached by changes in the outer appearance of the crystals and in surface modifications. Due to the fact that ibuprofen molecules can form hydrogen bonds, additives that can interact with these hydrogen bonds during the crystallization process can modify the properties of the resulting crystals.

Analgesics, Non-Narcotic↗

Differentiated thermal crystallization from amorphous chenodeoxycholic acid between the ground specimens derived from the polymorphs.

Crystallization behavior of amorphous chenodeoxycholic acid (CDCA) was studied using X-ray diffraction (XRD), infrared (IR) spectroscopy and differential scanning calorimetry (DSC). The two polymorphs of CDCA, form I (mp 166 degrees C) and form III (mp 119 degrees C), were ground with a vibrational mill. The ground samples of both crystal forms showed halo X-ray diffraction patterns. DSC curves of the amorphous samples derived from the form I and form III showed exothermic peaks due to the crystallization to the form I at 120 and 147 degrees C, respectively. When the ground form III was mixed with the ground form I, the crystallization temperature shifted to a lower temperature as the content of the ground form I increased. In the case of co-ground sample of form I and form III, the crystallization to form I crystals proceeded by two different modes. These results indicate that the physicochemical state was different among the ground samples of the form I and form III, and that the crystal nuclei played an important role on the crystallization process of the amorphous CDCA.

Calorimetry, Differential Scanning↗