Crystallization and preliminary X-ray characterization of a soybean seed lipoxygenase

An isoenzyme of soybean (Glycine max L. Merrill cv. Provar) lipoxygenase (EC 1.13.11.12) has been crystallized using the vapor diffusion method. Crystals were grown from solutions of the protein (7 mg/ml) using 10 to 20% (w/v) polyethylene glycol 8000 in citrate/phosphate buffer (pH 5.7) containing 0.5% (w/v) n-octyl-beta-D-glucopyranoside. The crystals reached maximum dimensions of 0.3 mm x 0.2 mm x greater than 2 mm. The enzyme crystallized in space group C222(1) with unit cell dimensions a = 246 A, b = 193 A and c = 75 A. A calculated Vm value of 2.35 A3/dalton was obtained assuming two molecules per asymmetric unit. The density of the crystals was found to be 1.16 g/ml, which confirmed the presence of two molecules per asymmetric unit and indicated a solvent content of 47.5%.     

A systematic approach to the large-scale production of protein crystals

Crystallization has recently emerged as a suitable process for the manufacture of biocatalysts in the form of cross-linked enzyme crystals (CLECs) or for the recovery of proteins from fermentation broths. In both instances it is essential to define conditions which control crystal size and habit, and that yield a reliable recovery of the active protein. Experiments to define the crystallization conditions usually depend on a factorial design (either incomplete or sparse matrix) or reverse screening techniques. In this work, we describe a simple procedure that allows the effect of three factors, for example protein concentration, precipitant concentration and pH, to be varied simultaneously and smoothly over a wide range. The results are mapped onto a simple triangular diagram where a 'window of crystallization' is immediately apparent, and that conveniently describes variations either in the crystal features, such as their yield, size, and habit, or in the recovery of biological activity. The approach is illustrated with two enzymes, yeast alcohol dehydrogenase (ADH I) and Candida rugosa lipase. For ADH the formation of two crystal habits (rod and hexagonal) could be controlled as a function of pH (6.5-10) and temperature (4-25 degrees C). At pH 7, in 10 to 16% w/v polyethylene glycol (PEG) 4000, only rod-shaped crystals formed whereas at pH 8, in 10 to 14% w/v PEG, only hexagonal crystals existed. For both enzymes, catalyst recovery was greatest at high crystallization agent concentrations and low protein concentration. For ADH, the greatest activity recovery was 87% whereas for the lipase crystals, by using 45% v/v 2-methyl-2,4-pentanediol (MPD) as the crystallization agent, a crystal recovery of 250 crystals per μl was obtained. For the lipase system, the use of crystal seeding was also shown to increase the crystal recovery by up to a factor of four. From the crystallization windows, the original conditions based on literature precedent (35% v/v MPD, 1 mM CaCl(2), 1.8 mg protein/ml) were altered (47.5% v/v MPD, 2 mM CaCl(2), 3 mg protein/ml). This led to an improved recovery of the lipase under conditions that scale reliably from 0.5 ml to 500 ml with no change in size, shape or recovery of the crystals themselves. Finally, these crystals were crosslinked with 5% v/v glutaraldehyde and mass and activity balances were calculated for the entire process of CLEC production. Up to 35% of the lipase activity present in the crude solid was finally recovered in the lipase CLECs after propan-2-ol fractionation, crystallization, and crosslinking.     

Crystallization and preliminary x-ray investigation of soybean beta-amylase.

Beta-Amylase [1, 4-alpha-D-glucan maltohydrolase, EC 3.2.1.2] has been purified from defatted soybean meal by fractional precipation with ammonium sulfate, ion-exchange chromatography on CM- and DEAE-Sephadex and gel filtration chromatography on Sephadex G-100. Two different components of beta-amylase were crystallized from ammonium sulfate solutions, and the homogeneity of each preparation was confirmed by sedimentation and disc electrophoretic analyses. Both components of soybean beta-amylase formed large single crystals (trigonal crystal system) from 40--50 per cent saturated ammonium sulfate solution buffered at pH 5.4 on dialyzing concentrated protein solution in the apparatus of Zeppezauer et al. Preliminary X-ray diffraction data gave a hexagonal lattice with unit cell dimensions a=86.1 A and c=144.4 A. The space group corresponds to P3121 or P3221, and one asymmetric unit contains one molecule of beta-amylase, assuming a crystal density of 1.25 g/ml and a molecular weight of the enzyme of 60,000 daltons. In this case, the crystal has a volume of 2.53 A-3 per atomic mass unit, and the percentage of protein in the crystal is about 52.     

Crystallization and preliminary X-ray crystallographic analysis of Mirabilis antiviral protein.

Mirabilis antiviral protein is a single-chain ribosome-inactivating protein purified from the tuberous root of Mirabilis jalapa L. We obtained several forms of crystals of the protein by the hanging drop vapor diffusion method, but most of these crystals were not suitable for X-ray crystallography. After refining the growth conditions, crystals of crystallographic quality were grown in 20-microliters droplets of an equi-volume mixture of 1.5% (w/v) protein solution and a reservoir solution containing 49 to 50% (w/v) ammonium sulfate and 50 mM-ammonium citrate (pH 5.4) at room temperature. Addition of 2 mM-adenine sulfate reduced twinning and "crystal shower". The resulting trigonal crystals diffract beyond 2.5 A resolution using a rotating anode X-ray generator. The space group was determined to be P3(1)21 or P3(2)21 (a = b = 103.9.A, c = 134.6 A, alpha = beta = 90 degrees, gamma = 120 degrees) based on their precession photography of h0l and hk0 zones. There seems to be three monomers in an asymmetric unit for VM = 2.51 A3/Da.     

Determination of molecular weight from protein crystals

Different methods for the determination, of molecular weight from protein crystals are summarized, and in some cases extended. The use of crystal density measurements is discussed, and several approaches based on such measurements, including density extrapolation (Colman &; Matthews, 1971) and crosslinking (Cornick et al., 1973), are described and illustrated by density measurements of crystals of γ-chymotrypsin and β-amylase. The importance of allowing for “bound water” in molecular weight estimation is illustrated by examples, and a summary is given of information which may be gained from densities of crystals soaked in heavy water.The determination of molecular weight from measurement of the loss of weight of crystals on drying is discussed and illustrated using North's (1959) data.Also the method of molecular weight estimation from “crystal volume and protein content” (Love, 1957; Heidner et al., 1971) is reviewed, and a new method based on “crystal mass and protein content” is proposed.     

Electron crystallographic analysis of two-dimensional streptavidin crystals coordinated to metal-chelated lipid monolayers.

Coordination of individual histidine residues located on a protein surface to metal-chelated lipid monolayers is a potentially general method for crystallizing proteins in two dimensions. It was shown recently by Brewster angle microscopy (BAM) that the model protein streptavidin binds via its surface histidines to Cu-DOIDA lipid monolayers, and aggregates into regularly shaped domains that have the appearance of crystals. We have used electron microscopy to confirm that the domains are indeed crystalline with lattice parameters similar to those of the same protein crystallized beneath biotinylated lipid monolayers. Although BAM demonstrates that the two-dimensional protein crystals grown via metal chelation are distinct from the biotin-bound crystals in both microscopic shape and thermodynamic behavior, the two crystal types show similar density projections and the same plane group symmetry.     

Crystallographic studies of protein denaturation and renaturation. 1. Effects of denaturants on volume and X-ray pattern of cross-linked triclinic lysozyme crystals

Triclinic crystals of hen egg-white lysozyme cross-linked with glutaraldehyde have been treated with various denaturants and found to be susceptible to x-ray structure analysis even after major conformational changes in the protein. Cross-linked crystals were isomorphous with the native form, and electron density difference maps indicated the locations of intermolecular corss-links, but showed no appreciable differences in the protein conformation. Soaking of the cross-linked crystals in danaturant solutions of increasing concentrations caused corresponding increases in crystal volume and decreases in minimum observable x-ray spacings. These changes proved partly reversible on diluting the solutions, and measurements of crystal volume and minimums x-ray spacing were used to follow denaturation and renaturation as a function of concentration for several denaturants. Some of these, including bromoethanol and sodium dodecyl sulfate, had little effect on the crystals below critical concentrations at which there was a sharp volume increase and loss of x-ray pattern, which could, however, be regenerated to about 3.2-A resolution. Others, including KCNS and urea, caused more gradual changes, but with a smaller degree of recovery. It is suggested that at least two different denaturation mechanisms are involved with detergent-like reagents disrupting the hydrophobic interactions joining the two wings of the lysozyme molecule and hydrophilic denaturants interacting primarily with polar groups on the molecular surface.     

Crucial steps in the structure determination of the Na+/H+ antiporter NhaA in its native conformation

Sodium proton antiporters are ubiquitous membrane proteins. Their importance for cell viability is the result of their role in homeostasis of intracellular pH, cellular Na+ content and cell volume. Recently, the first structure of this family of secondary transporters, namely of NhaA from Escherichia coli, revealed a novel fold and elucidated the molecular basis for the mechanism of transport and its regulation by pH. Here, we describe the key steps for the structure determination of NhaA, an iterative process of improving protein quality as well as crystallization conditions. Protein quality was optimized by shortening the purification to a single step and by changing the expression host. The major steps for crystal improvement were the exchange of the detergent during protein purification from the beta- to the alpha-anomer of DDM, the addition of OG to the crystallization set ups, and the growth of the crystals under conditions suitable for cryo-temperatures. Unexpectedly, the dimeric association of the transporter in the 3D crystal lattice is non-physiological. A comparison of the X-ray structure with the electron density map from cryo-electron microscopy of 2D crystals demonstrates that the NhaA helix packing in the 3D crystal is identical with the one in the lipid environment. Thus, the antiporter is in a native conformation in the 3D crystals.     

Structure, composition, and mechanical properties of shark teeth

The teeth of two different shark species (Isurus oxyrinchus and Galeocerdo cuvier) and a geological fluoroapatite single crystal were structurally and chemically characterized. In contrast to dentin, enameloid showed sharp diffraction peaks which indicated a high crystallinity of the enameloid. The lattice parameters of enameloid were close to those of the geological fluoroapatite single crystal. The inorganic part of shark teeth consisted of fluoroapatite with a fluoride content in the enameloid of 3.1 wt.%, i.e., close to the fluoride content of the geological fluoroapatite single crystal (3.64 wt.%). Scanning electron micrographs showed that the crystals in enameloid were highly ordered with a special topological orientation (perpendicular towards the outside surface and parallel towards the center). By thermogravimetry, water, organic matrix, and biomineral in dentin and enameloid of both shark species were determined. Dentin had a higher content of water, organic matrix, and carbonate than enameloid but contained less fluoride. Nanoindentation and Vicker's microhardness tests showed that the enameloid of the shark teeth was approximately six times harder than the dentin. The hardness of shark teeth and human teeth was comparable, both for dentin and enamel/enameloid. In contrast, the geological fluoroapatite single crystal was much harder than both kinds of teeth due to the absence of an organic matrix. In summary, the different biological functions of the shark teeth ("tearing" for Isurus and "cutting" for Galeocerdo) are controlled by the different geometry and not by the chemical or crystallographic composition.     

Determination of the protein content of crystals formed by Mastigocladus laminosus C-phycocyanin, Chroomonas spec. phycocyanin-645 and modified human fibrinogen using an improved Ficoll density gradient method

We demonstrated for several protein crystals of known protein content that the simple Ficoll density gradient method for crystal density determination as described by Westbrook (1976) often leads to quite erroneous results. In particular, the apparent density of loosely packed crystals can show a tremendous change within the first minutes of measurement. In order to derive the correct protein content the apparent crystal density must be followed as a function of time and has to be extrapolated back to the time of insertion of the crystal into the gradient. The packing densities of four novel protein crystals, formed by Mastigocladus laminosus C-phycocyanin, Chroomonas spec. phycocyanin-645 (two forms), and modified human fibrinogen have been determined and that of proteinase II of Crotalus adamanteus has been corrected. The C-phycocyanin crystals were found to contain (in contrast to earlier results reported by others) only one (alpha beta)-monomer, the phycocyanin-645 crystals two and three (alpha alpha' beta 2)-monomers, respectively, and the fibrinogen crystals one fibrinogen molecule per asymmetric unit.     

Strategies for the crystallization of viruses: using phase diagrams and gels to produce 3D crystals of Grapevine fanleaf virus

The small icosahedral plant RNA nepovirus Grapevine fanleaf virus (GFLV) is specifically transmitted by a nematode and causes major damage to vineyards worldwide. To elucidate the molecular mechanisms underlying the recognition between the surface of its protein capsid and cellular components of its vector, host and viral proteins synthesized upon infection, the wild type GFLV strain F13 and a natural mutant (GFLV-TD) carrying a Gly???Asp mutation were purified, characterized and crystallized. Subsequently, the geometry and volume of their crystals was optimized by establishing phase diagrams. GFLV-TD was twice as soluble as the parent virus in the crystallization solution and its crystals diffracted X-rays to a resolution of 2.7 ?. The diffraction limit of GFLV-F13 crystals was extended from 5.5 to 3 ? by growth in agarose gel. Preliminary crystallographic analyses indicate that both types of crystals are suitable for structure determination. Keys for the successful production of GFLV crystals include the rigorous quality control of virus preparations, crystal quality improvement using phase diagrams, and crystal lattice reinforcement by growth in agarose gel. These strategies are applicable to the production of well-diffracting crystals of other viruses and macromolecular assemblies.     

A stereologic electron microscope study of “tubular myelin figures” in alveolar fluids of rat lungs

Summary The three-dimensional structure of a composite material found in alveolar exudate of oxygen poisoned lungs but also present in normal lungs is stereologically analysed. It is composed of tubules of 450 Å diameter which are tightly packed in a quadratic lattice. The wall of the tub vile is formed by four-winged osmiophilic filaments which are located in the corners of the quadratic lattice; their interior is made up of a hydrophilic substance which contains either a tubule or a filament of moderate electron density. The osmiophilic substance of the walls is continuous with associated myelin figures which can be resolved into lamellae with a periodicity of 42 Å and can thus be considered to be water crystals of phospholipids. The nature of the content of the tubules, which presumably exerts the formative force on the phospholipid lamellae to form tubules, remains undetermined.Dedicated to Prof. W. Bargmann in honor of his 60th birthday.The research reported here has been sponsored by the Schweizerischer Nationalfonds zur Förderung der wissenschaftlichen Forschung (Nr. 2569); by the Stiftung für wissenschaftliche Forschung an der Universität Zürich; by the National Institutes of Health, USPHS, through grant RF-57; and the 6570th Aerospace Medical Research Laboratories under contract AF 61(052)-784 through the European Office of Aerospace Research (OAR), United States Air Force.     

Three dimensional structure of bacterial pili

Crystallographic and associated biochemical and structural studies are in progress on the fiber-forming pilin proteins of the gonococcal pilus. Preparative scale purification procedures have been developed for the gonococcal pilin protein, which appear generally applicable to bacterial pilins. For three gonococcal pilin protein strains, we have obtained both reassembled pilus fibers and three-dimensional crystals. One needle-shaped crystal form of gonococcal C30 pilin diffracts beyond 3 Å resolution using synchrotron x-ray radiation. A diffraction data set to 3.5 Å resolution has been collected on these needle-shaped crystals (lattice spacings a=125.4(3) b=120.4(3), c=26.61(4) Å) in which the packing arrangement of the pilin subunits appears to resemble that seen in the pilus fibers using electron microscopy. X-ray diffraction data confirm our proposed model for the overall polypeptide fold of a pilin subunit, which is an antiparallel 4- helix bundle similar to tobacco mosaic virus coat protein and myohemerythrin.     

Changes in the size and number of secretion granules in the rat exocrine pancreas induced by feeding or stimulation in vitro

Summary The size, number and volume per cell of secretion granules in rat exocrine pancreas have been measured using stereological techniques. The changes which occur as a result of feeding starved animals (90 min) or stimulating lobular fragments in vitro with carbachol are documented. In fasted animals mean acinar cell volume was estimated as 1670 m³ and the cells contained an average of around 450 secretion granules with a corrected mean diameter of 0.70 m. They occupied around 7% of cell volume. After feeding mean cell volume was about 1300 m³ and the cells contained an average of about 190 granules per cell with a mean diameter of 0.58 m. They occupied 3% of cell volume. A shift in the size frequency distribution of granule diameters occurred as a result of feeding. In vitro experiments in which lobules were induced to secrete with carbachol (10M, 3 h, 37° C) had a similar effect. Mean cell volume was reduced from around 1760 m³ to 1360 m³, mean granule number from around 420 per cell to 180 per cell and the volume density of granules was reduced from about 8% to 3% of cell volume. There was no significant change in mean granule diameter or shift in the size-frequency distribution of granule diameters. Incubation of tissues with cycloheximide (1 mM, 3 h, 37° C) did not prevent secretion by carbachol but it prevented replacement of granules. As a consequence, depletion by carbachol was greater in the presence of cycloheximide, the granules being reduced to around 110 per cell and to only 2.5% of cell volume. We conclude that feeding causes a preferential loss of larger granules and that during secretion replacement of granules occurs. Some of these granules are smaller than those evident in the glands of starved animals.     

Melting behaviour of A- and B-type crystalline starch

The melting behaviour of highly crystalline spherulites, of a short chain amylose DP-15 corresponding to both the A and B polymorphs of starch has been studied as a function of water content. At water contents >40% w/w A-type spherulites melt at temperatures approximately 20°C higher than B spherulites, whilst both crystal forms melt at lower temperatures in the presence of increasing amounts of water. Using the Flory Huggins relationship for polymer crystal melting in the presence of a diluent, it is possible to predict a value for the ideal melting temperature of the dry crystals of 530 K.     

Surface topography and molecular stoichiometry of the mitochondrial channel, VDAC, in crystalline arrays.

The mitochondrial outer membrane contains a protein, called VDAC, that forms large aqueous pores. In Neurospora crassa outer membranes, VDAC forms two-dimensional crystalline arrays whose size and frequency can be greatly augmented by lipase treatment of these membranes (C. Mannella, Science 224, 165, 1984). Fourier filtration and surface reconstruction of freeze-dried/shadowed (45 degrees) arrays produced detailed images of two populations of crystals, whose lattices are mirror images of each other. Most likely, this technique has revealed both surfaces of the same two-dimensional crystal with lattice parameters: a = 12.3 +/- 0.1 nm, b = 11.2 +/- 0.1 nm, and theta = 109 +/- 1 degree. Three-dimensional reconstructions of the surface reliefs on both sides of the crystal show them to be very similar. The majority of the protein forming the channel appears to be at or below the level of the membrane. To address the issue of the number of 30-kDa polypeptides that form a VDAC channel, measurements of mass per unit area were carried out by analyzing scanning transmission electron micrographs of unstained, freeze-dried arrays. The crystal form used for mass analysis contained the same motif of six stain-accumulating centers per unit cell, with p2 symmetry as in the oblique configuration, but it had a different orientation relative to the lattice lines. These data yielded a surface density of 1.9 +/- 0.2 kDa/nm2, indicating that there is a one-to-one ratio between VDAC polypeptides and the channels visualized in filtered electron micrographs, and that VDAC membrane crystals contain 68% protein and 32% lipid by mass.     

Crystallization and preliminary X-ray diffraction studies of Streptomyces phospholipase A2 in a calcium-binding form

Phospholipase A2 (PLA2) as a calcium-binding form, produced by Streptomyces violaceoruber, was crystallized in a form suitable for the diffraction analysis using the vapor diffusion method. Crystals were grown in 0.1 M Tris-HCl buffer (pH 8.5), 20 mM Ca2+ containing 50-60% (v/v) 2-methyl-2,4-pentanediol as a precipitant. They belong to the monoclinic space group P2(1), with the cell dimensions a=38.3 A, b=54.3 A, c=30.6 A, and beta=90.2 degrees. The crystals diffract the X-ray well and the diffraction intensity data were collected up to 1.6 A resolution. The crystal volume per unit mass, V(M) is 2.35 A3 Da(-1) with one molecule in the asymmetric unit, which corresponds to a solvent content of 47.7%.     

Solid-state cultivation of Chaetomium cellulolyticum on alkali-pretreated sawdust

Solid-state fermentations (78% initial moisture content) of alkali-pretreated Eastern Hard Maple sawdust were conducted in tray and tumble fermentors using chaetomium cellulolyticum. Crude protein content of the solids rose from 0.9 to 11% in the tray fermentor and 8% in the tumble fermentor in 20 days. These levels were almost equal to those achieved in corresponding slurry-state fermentations (1–5% (w/v)) of the same substrate. Specific growth rates were two to four times lower in the solid-state fermentors but this was offset by their greater solids-handling capacity: the rate of protein production per unit volume of fermentation mixture was comparable to that of the 5% (w/v) slurry and two to three times higher than that of the 1% (w/v) slurry.     

藤黄酸聚乳酸纳米粒的研制

以新型材料聚乳酸(PLA)为载体,研制出质量稳定的藤黄酸聚乳酸纳米粒(GA-PLA-NPs)乳液制剂,并对其安全性进行评价。采用改良的溶剂蒸发法制备藤黄酸聚乳酸纳米粒(GA-PLA-NPs);用透射电子显微镜（TEM）观察纳米粒的形态;用激光粒度分析仪测定其平均粒径大小和分布;经超速离心后用紫外分光光度计测定纳米粒的包封率与载药量;考察藤黄酸纳米粒的体外释放特性;经急性毒性实验考察藤黄酸纳米粒的安全性。得到确定处方工艺为：水相∶有机相为2∶1（v/v）,表面活性剂在有机相中的浓度为0.5%（w/v）,藤黄酸（GA）在有机相中的浓度为0.1%（w/v）,GA∶PLA为1∶4（w/w）。处方条件下制备的纳米粒平均粒径为51.36 nm;平均包封率与载药量分别为98.87%和13.3%;藤黄酸纳米粒的体外释药分为两相：突释期和缓释期;急性毒性试验测得藤黄酸纳米粒的ID50为26.3mg/kg。制备的藤黄酸聚乳酸纳米粒（GA-PLA-NPs）质量稳定、分散性良好。聚乳酸可能成为藤黄酸的新型载体。