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Negative staining of proteins.

Negative staining, some closely related alternative preparation techniques and radiation stability are considered. An attempt is made to clarify the mechanism of action and ultimate resolution limit of negative staining. The results of electron diffraction investigation of thermitase microcrystals embedded in glucose and glucose + stains are presented. It is shown that at doses not exceeding 10 electrons/nm2 electron diffraction from thermitase crystals demonstrate diffraction fields up to 0.2 nm. When adding heavy-atom salts to glucose or using negative staining, the relative intensities of reflections change and electron diffraction patterns for every type of heavy-atom additive (or negative stain) have their specific features. Such characteristic changes of reflection intensities indicate specific interaction of these additives (or stains) with the object. In the case of electron diffraction from the crystals stained using the routine negative staining technique the ordering was preserved down to 0.4-0.5 nm. Increasing the dose up to the normal value results in fading of distant reflections. Thus, negative staining with radiation doses less than the critical one could yield resolution down to 0.4 nm. Yet, the structure may change due to interaction with the stain. Nevertheless, the possibility that such resolution could be obtained for a limited number of objects should not be excluded. Some examples of the application of negative staining for investigation of quaternary and domain structure of proteins (nitrogenase, glutamine synthetase, mitochondrial ATP-synthase, membrane monooxygenase enzymes), tubular and two-dimensional protein crystals (catalase, phosphorylase, HWV protein, hydrogenase), as well as ribosomes and bacteriophages are given in the review.

Animals↗

Basal bodies of bacterial flagella in Proteus mirabilis. II. Electron microscopy of negatively stained material.

This paper investigates further the question of whether the flagella of Proteus mirabilis emerge from basal bodies. The bacteria were grown to the stage of swarmer differentiation, treated lightly with penicillin, and then shocked osmotically. As a result of this treatment, much of the cytoplasmic content and also part of the plasma membrane were removed from the cells. When such fragmented organisms were stained negatively with potassium phosphotungstate, the flagella were found to be anchored-often by means of a hook-in rounded structures approximately 50 mmicro wide, thus confirming Part I of our study. In these rounded structures a more brilliant dot was occasionally observed, which we interpret as being part of the basal granule. A prerequisite for the demonstration of the basal granules within the cells was, however, the removal of both the cytoplasm and the plasma membrane from their vicinity. In some experiments, the chondrioids were "stained" positively by the incorporation into them of the reduced product of potassium tellurite. The chondrioids were here observed to be more or less circular areas from which rodlike structures extended. The chondrioids adhered so firmly to the plasma membrane that they were carried away with it during its displacement by osmotic shocking, while the basal bodies were left behind. This observation disproves our previous suggestion that the flagella might terminate in the chondrioids. The basal bodies often occur in pairs, which suggest that they could be self-reproducing particles.

Cell Differentiation↗

The morphology of human immunodeficiency virus particles by negative staining electron microscopy.

Negative staining electron microscopy was used to examine culture fluids from the H9/HTLV-III cell line after concentration by centrifugation. Characteristic retrovirus-like particles bearing distinctive envelope projections were seen. The virion envelope was frequently extended in the form of a bleb or a tail. These particles were morphologically virtually indistinguishable from similar preparations of Friend murine leukaemia virus. H9/HTLV-III culture fluids contained, in addition, numerous comet-shaped particles with a dense head and flared tail. These particles were clumped by the addition of anti-HTLV-III-positive serum suggesting that they may represent intermediate forms of the virus.

Cell Line↗

The morphology of simian immunodeficiency virus as shown by negative staining electron microscopy.

Negative staining electron microscopy was used to study sucrose gradient-purified preparations of the simian immunodeficiency virus (SIVmac251). Both isolated and aggregated virus particles were observed together with some free-lying virus cores. The cores were 110 nm long and 25 to 50 nm wide and were mainly conical or wedge-like in shape. Surface projections were seen on the envelope membrane of many of the virus particles; the knobs were approximately 6 nm in length, 10 nm wide and from an end-on view they had a Y or triangular-shaped morphology.

Centrifugation, Density Gradient↗

Quantitative analysis of the mechanism of negative staining with native collagen fibrils and polar tropomyosin paracrystals.

The mechanism of formation of the negatively stained image in electron microscopy was infestigated with native collagen fibrils as a model. The negatively stained image was simulated from the primary structure by using the values of volume or bulkiness of each amino acid residue as a parameter for stain-excluding capacity. The pattern simulated from the bulkiness values gave an excellent fit with the negatively stained image. Since some contribution of positive staining components to negative staining has been suggested, positive staining with uranyl acetate was tested with various washing solutions of different pH. While acidic conditions did not produce any stained image, a positively stained image was easily obtained at alkaline pH. On the other hand, negatively stained images with stains of different charge character remained essentially the same as those obtained with acidic uranyl stains. It was concluded that the contribution of positive components to the negatively stained image is negligible under the conventional conditions for negative staining with uranyl acetate. In order to demonstrate the utility of the analytical method employing the values of "bulkiness," we studied the unknown molecular packing in the polar lead paracrystal of rabbit skeletal tropomyosin. Utilizing the primary sequence data for alpha-tropomyosin we successfully showed the polar paracrystal to be an array of molecules which are parallel and in register. Further, our analysis made it possible to deduce the position of a given residue in the negatively stained pattern of the polar paracrystal.

Amino Acids↗

Negative staining and genesis of D-periodicity in native collagen fibrils.

An investigation was carried out on the mechanism which gives rise to the banding exhibited by collagen fibrils after negative staining. The negative staining (phosphotungstic acid) band patterns of native collagen fibrils (type I), isolated from calf reticular dermis, were compared with computer-drawn band patterns. The stimulations were based on the primary structure of bovine type I collagen, the "quarter stagger" molecular packing and different conformations of telopeptides. The results suggest that in negative staining, the stain exclusion effect depends on both spatial factors and water repelling factors being the "bulkiness" (molecular volume/length ratio) as well as the hydrophobicity of the amino acids of alpha 1 (I) and alpha 2 (I) chains directly involved. No final conclusion could be drawn about the contribution of positive staining to negative staining. Improvements in the simulations were achieved when the telopeptides were shaped according to particular conformational models.

Animals↗

Stacking in lipid vesicle-tubulin mixtures is an artifact of negative staining.

Multilamellar stacking seen in negatively stained lipid vesicle-tubulin mixtures has been attributed to lipid-protein interactions (Caron, J. M., and R. D. Berlin, 1979, J. Cell Biol. 81:665-671). We show that this stacking is produced by the phosphotungstic acid used for staining, independent of the presence of tubulin in the sample. The morphology of negatively stained single bilayer vesicles obtained from dimyristoyl phosphatidylcholine or egg lecithin is specifically dependent upon the choice of metal stain. Uranyl oxalate maintains the appearance of unilamellar vesicles. After staining with sodium tungstate, the lipids form a network of multilayered lamellae with a periodicity of approximately 55 A. Phosphotungstic acid produces stacks of flattened vesicles with a period of approximately 115 A as well as broader multilamellar structures having a 55 A repeat. The stain-determined morphology is not markedly altered by sample concentration, incubation time, or temperature, or by the presence of tubulin.

Lipoproteins↗

Cryo-negative staining.

A procedure is presented for the preparation of thin layers of vitrified biological suspensions in the presence of ammonium molybdate, which we term cryo-negative staining. The direct blotting of sample plus stain solution on holey carbon supports produces thin aqueous films across the holes, which are routinely thinner than the aqueous film produced by conventional negative staining on a continuous carbon layer. Because of this, a higher than usual concentration of negative stain (ca. 16% rather than 2%) is required for cryo-negative staining in order to produce an optimal image contrast. The maintenance of the hydrated state, the absence of adsorption to a carbon film and associated sample flattening, together with reduced stain granularity, generates high contrast cryo-images of superior quality to conventional air-dry negative staining. Image features characteristic of unstained vitrified cryo-electron microscopic specimens are present, but with reverse contrast. Examples of cryo-negative staining of several particulate biological samples are shown, including bacteriophage T2, tobacco mosaic virus (TMV), bovine liver catalase crystals, tomato bushy stunt virus (TBSV), turnip yellow mosaic virus (TYMV), keyhole limpet hemocyanin (KLH) types 1 and 2, the 20S proteasome from moss and the E. coli chaperone GroEL. Densitometric quantitation of the mass-density of cryo-negatively stained bacteriophage T2 specimens before and after freeze-drying within the TEM indicates a water content of 30% in the vitreous specimen. Determination of the image resolution from cryo-negatively stained TMV rods and catalase crystals shows the presence of optical diffraction data to ca. 10 A and 11.5 A, respectively. For cryo-negatively stained vitrified catalase crystals, electron diffraction shows that atomic resolution is preserved (to better than 20 diffraction orders and less than 3 A). The electron diffraction resolution is reduced to ca. 10 A when catalase crystal specimens are prepared without freezing or when they are freeze-dried in the electron microscope. Thin vitrified films of TMV, TBSV and TYMV in the presence of 16% ammonium molybdate show a clear indication of two-dimensional (2-D) order, confirmed by single particle orientational analysis of TBSV and 2-D crystallographic analysis of TYMV. These observations are in accord with earlier claims that ammonium molybdate induces 2-D array and crystal formation from viruses and macromolecules during drying onto mica. Three-dimensional analysis of the TBSV sample using the tools of icosahedral reconstruction revealed that a significant fraction of the particles were distorted. A reconstruction from a subset of undistorted particles produced the characteristic T = 3 dimer clustered structure of TBSV, although the spikes are shortened relative to the structure defined by X-ray crystallography. The 20S proteasome, GroEL, catalase, bacteriophage T2, TMV, TBSV and TYMV all show no indication of sample instability during cryo-negative staining. However, detectable dissociation of the KLH2 oligomers in the presence of the high concentration of ammonium molybdate conforms with existing knowledge on the molybdate-induced dissociation of this molecule. This indicates that the possibility of sample-stain interaction in solution, prior to vitrification, must always be carefully assessed.

Animals↗

Gap junction structures. VII. Analysis of connexon images obtained with cationic and anionic negative stains.

Micrographs of isolated gap junction specimens, negatively stained with one molybdate, three tungstate and three uranyl stains, were recorded at low and high irradiation. Fourier-averaged images of the negatively stained gap junctions have been self-consistently scaled to identify conserved and variable features. Intrinsic features in the hexagonally averaged images have been distinguished from residual noise by statistical comparisons among similarly prepared specimens. The cationic uranyl stains can penetrate the axial connexon channel, whereas the anionic stains are largely excluded; these observations indicate that the channel is negatively charged. Variability in the extent of the axial stain penetration, and enhancement of this staining by radiation damage and heating may be accounted for by a leaky, labile channel gate. The peripheral stain concentrations marking the perimeter of the skewed, six-lobed connexon image and the stain-excluding region at the 3-fold axis of the lattice, which are seen only under conditions of low irradiation with both anionic and cationic stains, are identified as intrinsic features of the isolated gap junction structure. The stain concentrations located approximately 30 A from the connexon center appear to be symmetrically related on opposite sides of the junction by non-crystallographic 2-fold axes oriented approximately 8 degrees to the lattice axes at the plane of the gap. The radiation-sensitive hexagonal features seen in the negatively stained images may correspond to substructure on the cytoplasmic surfaces of the paired gap junction membranes.

Animals↗

Ultrastructure of glomerular basement membrane in active heymann nephritis rats revealed by tissue-negative staining method.

Recently, we have developed a tissue-negative staining method, and successfully visualized fine meshwork structure of the glomerular basement membrane (GBM). To clarify the mechanism of proteinuria in active Heymann nephritis, we performed tissue-negative staining and investigated the ultrastructural alterations of the GBM. Active Heymann nephritis, the animal model of human membranous nephropathy, was induced in Lewis rats by the injection of proximal tubular brush border antigen, i.e. Fx1A. Urinary protein excretion was measured and histological studies were performed over 15 weeks following the Fx1A injection. Proteinuria developed at 10 weeks after injection (38.2 +/- 7.4 mg/day) and progressively increased (160.2 +/- 20.6 mg/day at 15 weeks). Capillary fine deposits of IgG and C3 were seen by immunofluorescence, and subepithelial electron dense deposits (EDD) by transmission electron microscopy (TEM). Using the tissue-negative staining method, regular meshwork structure consisted of fine fibrils and pores (2.5 +/- 0.7 nm in short dimension) was observed in the GBM of control rats. At 10 and 15 weeks after injection, the GBM, directly facing the endothelial side of EDD, contained enlarged pores and nephrotic tunnels. Mean values of the short dimension of enlarged pores were 2.9 +/- 0.5 nm at 10 weeks and 3.1 +/- 0.4 nm at 15 weeks, which were significantly larger than that of control rats (p < 0.01). The rest area of the GBM, including newly produced GBM covering the epithelial side of EDD, had no significant difference in size of the pores from control GBM and no tunnels. Although there was no significant difference in the size of enlarged pores between 10 and 15 weeks, the percentage area of GBM with impaired size barrier increased at 15 weeks (51.4 +/- 8.1%) compared with 10 weeks (24.0 +/- 8.3%) and related to severity of proteinuria. The density of the tunnels also increased at 15 weeks. In conclusion, immune deposits may affect the GBM biosynthesis and induce the defect of size barrier of the GBM, which is responsible for proteinuria in active Heymann nephritis.

Animals↗

Functional and structural analysis of acetylcholine receptor-rich membranes after negative staining.

Phosphotungstate (pH 7.4) used for negative staining of membranes from Torpedo electric tissue rich in acetylcholine receptor does not affect binding properties and cation permeability of the receptor and its ion channel. Uranyl salts, frequently used for negative staining, precipitate the receptor-rich membranes making measurements of ligand binding and ion-permeability regulation impossible. The gross ultrastructure in the two stains is not significantly different, but for future high-resolution electron microscopy aiming at visualizing structural details of functional receptor molecules it is necessary to resort to a stain preserving native and active receptor. Uranyl salts are not applicable for this purpose. The electron micrographs obtained with phosphotungstate reveal two distinct structures in the receptor-rich membrane: a closed ring ('doughnut') and an open ring ('horseshoe'), with a ratio of abundance of about 3:2.

Acetylcholine↗

Visualization of domains in native and nucleotide-trapped myosin heads by negative staining.

Electron microscopy of negatively stained vertebrate skeletal muscle myosin molecules has revealed substructure suggestive of globular domains in the head portions of the molecule. This head substructure has been examined after both low and high electron doe. The results suggest it is probably not an artefact of radiation damage. The most common appearance is of one or two stain-filled clefts which run roughly perpendicular to the long axis of the head, giving rise to the appearance of two or three domains in a line. A large domain is located at the end of the head, while two smaller domains are arranged between this and the head-tail junction. The size of the large distal domain (about 10 nm long and about 7 nm wide at its widest point) is similar in heads showing either two or three domains. Stable analogues of M.ATP and M.ADP.Pi, the predominant complexes present during hydrolysis of ATP by myosin, were prepared by crosslinking the two reactive SH groups (SH1 and SH2) in the myosin head heavy chain with N,N'-p-phenylenedimaleimide (pPDM) in the presence of ADP, and by forming a complex with vanadate ion and ADP. At this resolution (approximately 2 nm) the heads of these modified molecules did not appear markedly different from those of the untreated protein, although there was a small increase in the number of straight as opposed to curved heads after cross-linking with pPDM.

Animals↗

Topography of the myosin molecule as visualized by an improved negative staining method.

An improved negative staining method has been used to visualize monomeric myosin molecules. Each lobe (subfragment 1) of the molecule looked like an elongated pear, and the widths of the thick and thin portions were about 95 and 55 A, respectively. The length of each lobe was about 210 A. It appeared capable of moving azimuthally and altitudinally, utilizing its juncture with the rod portion as the base. The rod portion of the molecule was about 1400 A long and 30 A wide. It also appeared to possess a considerably flexible region at a point about 680 A from the tail-end.

Animals↗

[Ultrastructure of Sarcocystis tenella. I. Endozoïte (after negative staining)].

The employment of negative staining technics for the endozoites (cyst stages) of Sarcocystis tenella allowed the elucidation of certain aspects of their fine structure. The conoid consists of similar to 20 oblique fibers and is surmounted by a ring with regular ornamentation. In the conoid's interior there are 2 excentric parallel microtubules which extend posteriorly for a considerable distance into the adjacent cytoplasm. The fibers of the conoid, intraconoid microtubules, appear to have the same diameter and structure as the 22 subpellicular microtubules. They are "cemented" anteriorly into a periconoidal ring which surrounds the conoid. The "reticulated" pellicle has certain differentiations: the micropore, surrounded by a "fibrillar" element, similar to 10 subcircular structures arranged into an anterior crown, and 11 rows of granules converging toward the posterior end. The sarconemes look like rice grains which, contrary to previous statements, are independent of one another. It is established that there are only 2 rhoptries.

Cell Membrane↗

Negative staining characteristics of arrays of mitochondrial pore protein: use of correspondence analysis to classify different staining patterns.

Fourier-filtered images of negatively stained arrays of mitochondrial pore protein have been classified by correspondence analysis of their diffraction patterns. The most significant component of interpattern variation is an isotropic shift in reflection intensities between high- and low-order reflections. This corresponds in the images to the presence or absence of high resolution detail (stain minima). Experimentally the loss of detail in images correlates with the use of highly dissociated heavy metal salts as negative stains. It is proposed that such stains yield poorer negative-contrast images due to electrostatic binding of heavy-metal complex ions to fixed charge groups on the protein. Results with surface-modified protein arrays are consistent with this hypothesis.

Crystallography↗

Ultrastructural alterations of the mitochondrial ATPase in the calcium paradox as revealed by negative staining.

We have used a simple negative staining technique to study the structural alterations of mitochondria from biopsies of hearts subjected to the calcium paradox and treatment with diltiazem, a calcium channel blocker. A significant (P less than 0.05) decrease in the number of spheres on the mitochondrial membranes occurs during the calcium paradox (58.0 +/0 4.1/micrometer vs. control 80.5 +/- 6.5). Treatment with diltiazem prevented the loss of spheres from mitochondrial membranes during the calcium paradox (75.5 +20 5.0 micrometer). We found that this negative staining technique can be used for quick assessment of the condition of mitochondria in biopsies from normal and pathological organs.

Adenosine Triphosphatases↗

C-reactive protein is useful in distinguishing Gram stain-negative bacterial meningitis from viral meningitis in children.

OBJECTIVE: To clarify to what extent Gram stain-negative bacterial meningitis can be distinguished from viral meningitis by assessment of cerebrospinal fluid (CSF) and blood indices and serum C-reactive protein (CRP) in children over 3 months of age. DESIGN: Common CSF indices, blood leukocyte counts, and serum CRP values were compared between patients with bacterial meningitis who had a positive CSF bacterial culture but a negative Gram stain and patients with viral meningitis. POPULATION: Three hundred twenty-five consecutive patients with CSF culture-proven bacterial meningitis, for whom Gram stain was negative in 55 cases, and 182 children with proven or presumed viral meningitis. RESULTS: Significant differences between patients with bacterial and viral meningitis were found in all indices with large overlap in all except serum CRP. In patients with bacterial meningitis, the mean CSF glucose concentration, protein concentration, leukocyte count, blood leukocyte count, and serum CRP were 2.9 mmol/L (52 mg/dL), 1.88 g/L, 4540 x 10(6)/L, 18.0 x 10(9)/L, and 115 mg/L; and in those with viral meningitis, mean values were 3.3 mmol/L (59 mg/dL), 0.52 g/L, 240 x 10(6)/L, 10.6 x 10(9)/L, and <20 mg/L, respectively. Of the tests investigated in this study, only serum CRP was capable of distinguishing Gram stain-negative bacterial meningitis from viral meningitis on admission with high sensitivity (96%), high specificity (93%), and high negative predictive value (99%). CONCLUSION: Exclusion of bacterial meningitis with only the conventional tests is difficult. Combined with careful physical examination and CSF analyses, serum CRP measurement affords substantial aid.

Adolescent↗

Effects of phosphotungstate negative staining on the morphology of the isolated Golgi apparatus.

Isolated Golgi complexes can be recognized in phosphotungstate (PTA) negative stain as stacks of membranous plates surrounded by a complex anastomosing network of tubules and vesicles. The extent of this tubular network is, however, much greater than can be observed in thin sections of whole cells. To determine which of the steps leading to the final negatively stained image may produce the observed changes, we have monitored each of the steps by other electron microscope and biochemical methods. The first damage to the membranes seems to occur during the initial isolation procedure as judged by the appearance of smooth patches on the freeze-fractured membrane faces that are normally covered with particles. Subsequent suspension of the Golgi fraction in water, to dilute the sucrose for negative staining, leads to the disappearnce of the stacking, to some tubulation and some vesiculation of the membranes as judged by thin section and freeze-cleave microscopy. The latter technique also reveals an increase in smooth-cleaving membrane faces. Application of the negative stain to the water-washed Golgi fraction, finally, produces extensive tubular arrays and a simultaneous decrease in the remaining large membranous vesicles. The freeze-cleaved tubular membranes appear essentially smooth except for small patches of aggregated particles. Parallel gel electrophoresis studies of the membranes and of the water and negative stain wash extracts indicate that protein extraction is involved in these morphological changes. PTA seems to be a particularly effective solvent for certain membrane proteins that are not removed by the water wash. These observations suggest that removal of membrane proteins alters structural restraints on the membrane lipids so that they behave semiautonomously like myelinics and form new artificial structures. This does not eliminate the possibility, however, that some tubules also exist in the Golgi apparatus in vivo.

Animals↗