Sputter shadowing

A device has been constructed which allows specimens to be shadowed in a conventional sputter water. This process of sputter shadowing lends to specimens a contrast suitable for imaging in the transmission electron microscope (TEM). The process has the practical advantages over metal evaporation shadowing of lower instrumentation costs, less user training, and less time expenditure per shadowing operation. It provides on a single grid a spectrum of shadowing contrasts from which optimal imaging for a particular specimen can be chosen. The process minimizes radiant and metal deposition heating of the specimen and, thereby, may better preserve its structure during the contrasting procedure. The grain resulting from sputter shadowing differs significantly from that obtained by metal evaporation shadowing and the possibility for using this difference to improve resolution in shadowed preparations is discussed.     

AN ultrastructural study of cross-bridge arrangement in the frog thigh muscle thick filament.

We have developed thick filament isolation methods that preserve the relaxed cross-bridge order of frog thick filaments such that the filaments can be analyzed by the convergent techniques of electron microscopy, optical diffraction, and computer image analysis. Images of the filaments shadowed by using either unidirectional shadowing or rotary shadowing show a series of subunits arranged along a series of right-handed near-helical strands that occur every 43 nm axially along the filament arms. Optical filtrations of images of these shadowed filaments show 4-5 subunits per half-turn of the strands, consistent with a three-stranded arrangement of the cross-bridges, thus supporting our earlier results from negative staining and computer-image analysis. The optical diffraction patterns of the shadowed filaments show a departure from the pattern expected for helical symmetry consistent with the presence of cylindrical symmetry and a departure of the cross-bridges from helical symmetry. We also describe a modified negative staining procedure that gives improved delineation of the cross-bridge arrangement. From analysis of micrographs of these negatively stained filament tilted about their long axes, we have computed a preliminary three-dimensional reconstruction of the filament that clearly confirms the three-stranded arrangement of the myosin heads.     

Electron microscopy and computer image averaging of ice-embedded large ribosomal subunits from Escherichia coli

Electron micrographs of frozen-hydrated, large ribosomal subunits from Escherichia coli have been analyzed by computer image processing. Images of subunits in the so-called "crown" orientation were analyzed by correlation alignment procedures developed for negatively stained specimens. Averages of the aligned images showed both similarities and differences to averages determined for negatively stained specimens. The L1 ridge is more dense and stalk-like in frozen-hydrated as compared with negatively stained subunits, possibly because it is associated with ribosomal RNA. The results show that it should be feasible to determine the three-dimensional structure of the large ribosomal subunit from micrographs of individual, frozen-hydrated subunits that have been tilted in the electron microscope.     

Two-dimensional crystals of a membrane protein: arrangement of subunits within the crystal sheet

Two-dimensional crystals have been prepared from the photosynthetic reaction center of Rhodopseudomonas viridis. Filtered images of these crystals show individual subunits approximately 4.5 nm in diameter arranged at a center-to-center distance of 6.4 nm. Our previous studies suggested that each subunit within such a sheet corresponds to a single photosynthetic reaction center. Air-dried and freeze-etched shadowed preparations of the crystals yield images which are quite different from negatively stained material. Rotary-shadowed surfaces of the crystals show rows of wedge-shaped particles separated by 3 nm furrows. Two such wedge-shaped particles occupy the 12.1 X 12.9 nm area in which four negatively stained subunits are normally visualized. Close analysis of these shadowed pictures suggests that both the shadowed and negatively stained images can be accounted for by a single model of subunit arrangement within the crystal. Within each 12.1 X 12.9 nm unit cell, two subunits are placed near one surface of the sheet, and two others are near the other surface. All four subunits are visible in negative stain. When the surface is shadowed, only the two subunits which project above the surface of the sheet accumulate appreciable amounts of the heavy metal shadow. Because of their close position, one subunit shades the other, forming the wedge-shaped appearance characteristic of the crystal. The only arrangement consistent with both shadowed and negatively stained images is one in which the two raised subunits occupy positions at either end of a diagonal across the unit cell. The analysis of shadowed images indicates that the plane group of the crystals is P22(1)2(1).     

Use of wolfram trioxide for setting off preparations of nucleic acids

The use of tungsten trioxide for shadowing nucleic acids is shown to be possible. Approximately 20 mg of tungsten trioxide could be prepared by heating (25 s, 2 V) a coil (4 turns, 1.5 mm i.d.) made of tungsten wire 0.5 mm diameter in a vacuum evaporator at atmospheric pressure. As revealed by electron microscopy, this amount of tungsten trioxide is sufficient for qualitative rotary shadowing phage lambda DNA.     

THE SIZE OF THE CELLULOSE MICROFIBRIL

Recently the lateral width of the cellulose microfibril has been estimated as 30 A rather than about 150 to 200 A, by extrapolation of data from model shadowing experiments. The difference was attributed to a layer of metal deposited during shadowing. However, direct photographs of the same microfibrils parallel and perpendicular to the direction of shadowing, of unshadowed portions of microfibrils compared with shadowed portions of the same microfibrils, of silver-stained unshadowed microfibrils, and of unshadowed, unstained segments of microfibrils give no evidence of a layer of metal of this thickness in material shadowed under normal conditions. Furthermore, the evidence for microfibril strands of about 35 A in width from negative-staining experiments is subject to a bias from the form of the filaments and from variable positive adsorption of phosphotungstic acid by cellulose. Consequently, the conclusion that the true lateral width of native cellulose microfibrils is about one-fifth of the presently accepted value is not yet justified by unequivocal direct experimental evidence.     

Structure of the Escherichia coli 50 S ribosomal subunit

Freeze-dried and shadowed Escherichia coli 50 S ribosomal subunits have been examined by electron microscopy and a model of the subunit has been constructed. High resolution shadow casting has enabled us to determine independently the absolute hand of the subunit and to reveal some new structural features.     

Macromolecular structure and aggregation states of Helicobacter pylori urease.

Urease purified from Helicobacter pylori by differential ultracentrifugation and fast pressure liquid chromatography was composed of subunits with apparent molecular weights (MrS) of 66,000 and 30,000. Electron microscopy of this purified material demonstrated that it formed disc-shaped macromolecular aggregates that were approximately 13 nm in diameter and 3 nm thick. Images of both negatively stained and shadowed preparations indicated that the discs tended to stack to form pairs and then these pairs further aggregated to form four-disc stacks. This stacking of subunits explains the heterogeneity observed previously in the molecular weight of urease preparations. In some negatively stained preparations there were also some smaller (approximately 8-nm-diameter) annular units present, which may represent individual urease units or possibly an aggregate of one of the two subunits from which urease is constructed.     

Atomic force microscopy of mammalian sperm chromatin

We have used the atomic force microscope (AFM) to image the surfaces of intact bull, mouse and rat sperm chromatin and partially decondensed mouse sperm chromatin attached to coverglass. High resolution AFM imaging was performed in air and saline using uncoated, unfixed and unstained chromatin. Images of the surfaces of intact chromatin from all three species and of an AFM-dissected bull sperm nucleus have revealed that the DNA is organized into large nodular subunits, which vary in diameter between 50 and 100 nm. Other images of partially decondensed mouse sperm chromatin show that the nodules are arranged along thick fibers that loop out away from the nucleus upon decondensation. These fibers appear to stretch or unravel, generating narrow smooth fibers with thicknesses equivalent to a single DNA-protamine complex. High resolution AFM images of the nodular subunits suggest that they are discrete, clipsoid-shaped DNA packaging units possibly only one level of packaging above the protamine-DNA complex.     

Helical Filaments of Human Dmc1 Protein on Single-Stranded DNA: A Cautionary Tale

Proteins in the RecA/Rad51/RadA family form nucleoprotein filaments on DNA that catalyze a strand exchange reaction as part of homologous genetic recombination. Because of the centrality of this system to many aspects of DNA repair, the generation of genetic diversity, and cancer when this system fails or is not properly regulated, these filaments have been the object of many biochemical and biophysical studies. A recent paper has argued that the human Dmc1 protein, a meiotic homolog of bacterial RecA and human Rad51, forms filaments on single-stranded DNA with ∼ 9 subunits per turn in contrast to the filaments formed on double-stranded DNA with ∼ 6.4 subunits per turn and that the stoichiometry of DNA binding is different between these two filaments. We show using scanning transmission electron microscopy that the Dmc1 filament formed on single-stranded DNA has a mass per unit length expected from ∼ 6.5 subunits per turn. More generally, we show how ambiguities in helical symmetry determination can generate incorrect solutions and why one sometimes must use other techniques, such as biochemistry, metal shadowing, or scanning transmission electron microscopy, to resolve these ambiguities. While three-dimensional reconstruction of helical filaments from EM images is a powerful tool, the intrinsic ambiguities that may be present with limited resolution are not sufficiently appreciated.     

An initial test of a method for the estimation of real mean particle size from shadowed samples

During shadowing, a "cap" of metal develops on small particles. This cap increases apparent particle with (measured normal to the shadowing direction) by an extent which cannot be predetermined. The extent of this increase in particle size (here defined as the "cap," X) is estimated in the present method by using opposite (180 degrees sample rotation) bidirectional shadowing. It is argued that the bidirectional cap is the sum of the two unidirectional caps, and therefore that X = 2A - (B + C), where A is the mean bidirectionally shadowed particle size, and B and C are the two mean unidirectionally shadowed particle sizes. As a validation of the method, the mean diameter of air-dried ferritin was estimated and the results appear to confirm the hypothesis (mean diameter by present method, 10.7 +/- 0.2 nm; mean diameter by previous methods, 10.89 nm).     

Hochauflösende Gefrierätzung

Zusammenfassung Die Anwendungsmöglichkeit der Gefrierätztechnik auf molekularbiologische und cytochemische Probleme ist vielfach durch das zu geringe Auflösungsvermögen der derzeit üblichen Simultanbeschattung mit Platin-Kohle begrenzt. Zwar lassen sich durch Beschatten mit höchstschmelzenden Metallen Abdrucke mit höherer Auflösung erzielen, jedoch scheinen bisher alle Versuche, diese Methode in der Gefrierätzung anzuwenden, fehlgeschlagen zu sein, da sie zu Präparatveränderungen führten. Außer hoher Auflösung müssen nämlich Beschattungsmethoden, um für die Gefrierätzung geeignet zu sein, auch folgende Bedingungen erfüllen: kurze Aufdampfzeit, geringe thermische Präparatbelastung und große chemische Stabilität des Abdruckes. Durch die Verwendung von Tantal-Wolfram als Aufdampfmaterial und die Konstruktion eines geeigneten Elektronenstrahl-Verdampfers, der eine Reduzierung der Wärmestrahlung und ein Ausschalten des Ionenbeschusses ermöglicht, ist es nunmehr gelungen, obige Bedingungen zu erfüllen und die Beschattung mit höchstschmelzenden Metallen auch in der Gefrierätzung erfolgreich einzusetzen. Die mit Tantal-Wolfram beschatteten Präparate sind entsprechenden Platin-Kohle-Abdrucken an Auflösung deutlich überlegen.Da die Wärmebelastung des Präparates in der Gefrierätztechnik von entscheidender Bedeutung ist, wurde sie für Ta/W und Pt/C-Beschattungen untersucht. Bei Ta/W-Be-dampfung liegt der für unsere Anordnung berechnete Wärmefluß bei 16 mW·cm^–2, der gemessene beträgt 23 mW·cm^–2. Bei Pt/C-Verdampfung ist die berechnete Wärmebelastung gleich hoch wie bei Ta/W. Der an einem üblichen Verdampfer gemessene Wärmefluß beträgt aber 41 mW·cm^–2. Rechnung und Experiment stimmen darin überein, daß die Versuchsbedingungen, wie Aufdampfrate, Verdampfergröße und -abstand auf die thermische Präparatbelastung einen stärkeren Einfluß haben, als die Art des aufgedampften Materials.

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Improved resolution in freeze-etching

Summary Resolution in freeze-etching is primarily limited by the need for shadowing the replica. In addition to giving high resolution, any technique suitable for freeze-etching must allow short shadowing times, a low thermal load for the specimen, and must provide a final film capable of surviving the drastic chemical procedures used for cleaning the replica.Simultaneous evaporation of platinum and carbon is at present the standard shadowing method in freeze etching. Replicas of higher resolution can in principle be obtained by using very high melting metals such as tungsten or tantalum. Extensive specimen damage caused by long evaporation times and excessive thermal load have however prevented the successful application of such ultrashadowing methods to freeze etching.Since neither long shadowing times nor a high thermal load are properties intrinsic to ultrashadowing, a suitable electron beam evaporator for high melting metals was built and thus ultrashadowing successfully applied to freeze-etching. All parts of the gun are water cooled and can be outgased by electron bombardment. The source can thus be operated reproducibly at high rates and without affecting the vacuum. The actual source (3 mm Ø) is the only hot part of the gun not shielded from the specimen. The ions which are generated during evaporation, and can cause considerable specimen damage, are deflected from the specimen by an electric field. The evaporation is done in 7–10 seconds, the source-specimen distance is 200 mm. For the shadowing material we use a tantalum-tungsten alloy. The resultant films are stable in 70% sulfure acid.At lower magnification freeze-etched specimen which are shadowed with Ta/W look just like Pt/C replicas which indicates that no additional artification took place. High magnification micrographs of ultrashadowed objects show a resolution considerably higher than those of platinum-carbon replicas published in the literature.Since heat damage is a crucial problem in freeze-etching the thermal load for tantalum-tungsten-and platinum-carbon-shadowing was calculated. For both methods a theoretical value of approximately 16 mW·cm^–2 was obtained provided the above shadowing conditions are observed and the ions are deflected from the specimen. Furthermore, the calculations show that the load caused by thermal radiation can be reduced drastically, without increasing the shadowing time, if the gun is operated at a higher rate thus allowing the use of either a smaller source or a longer source-specimen distance.Measurements of the thermal load agreed basically with the calculations. The values measured using the tantalum-tungsten gun were about half the ones obtained during platinum-carbon shadowing with a commercial evaporator.

     

Characteristic views of prokaryotic 50S ribosomal subunits

Summary Multivariate statistical analysis and classification techniques are powerful tools in sorting noisy electron micrographs of single particles according to their principal features, enabling one to form average images with an enhanced signal-to-noise ratio and a better reproducible resolution. We apply this methodology here to determining the characteristic views of the large (50S) ribosomal subunits from the eubacteriumEscherichia coli and the archaebacteriaMethanococcus vannielii, Sulfolobus solfataricus, andHalobacterium marismortui. Average images were obtained of the subunit in the common crown and kidney projections, but views of the particle in orientations intermediate between these two extremes were also elucidated for all species. These averages show reproducible detail of up to 2.0 nm resolution, thus enabling the visualization and interspecies comparison of many structural features as a first step toward comparing the actual three-dimensional structures. Our results disprove evolutionary lineages recently postulated on the basis of electron microscopical images of ribosomal subunits.     

Targeting exposed RNA regions in crystals of the small ribosomal subunits at medium resolution.

Within the framework of ribosomal crystallography, the small subunits are being analyzed, using crystals diffracting to 3 A resolution. The medium resolution electron density map of this subunit, obtained by multiple isomorphous replacement, show recognizable morphologies, strikingly similar to the functional active conformer of the small ribosomal subunit. It contains elongated dense features, traceable as RNA chains as well as globular regions into which the structures determined for isolated ribosomal proteins, or other known structural motifs were fitted. To facilitate unbiased map interpretation, metal clusters are being covalently attached either to the surface of the subunits or to DNA oligomers complementary to exposed ribosomal RNA. Two surface cysteines and the 3' end of the 16S ribosomal RNA have been localized. Targeting several additional RNA regions shed light on their relative exposure and confirmed previous studies concerning their functional relevance.     

Time-Lapse Imaging of Conformational Changes in Supercoiled DNA by Scanning Force Microscopy

Most of the scanning force microscopy (SFM) images of supercoiled DNA on untreated mica thus far reported have not shown tight plectonemic structure seen by electron microscopy, but instead less coiled molecules and sometimes a partly "condensed" state with intimate chain-chain interactions. By observing time-lapse images of conformational changes of DNA induced by decreasing ionic strength of imaging buffer in solution SFM, we could show that the process of water rinsing, an indispensable step for preparation of dried samples, may be responsible for some of the conformational anomalies in the images previously reported. We have studied several protocols to observe supercoiled DNA molecules by SFM and discuss the merits and the demerits. Images obtained following uranyl acetate treatment may be ideal for the detection of DNA damage, as the supercoiled and nicked forms are easily distinguishable.     

Scanning tunnelling microscopy of 16S ribosomal RNA in water

The scanning tunnelling microscope has been used to image 16S ribosomal RNA molecules in water electrophoretically deposited on graphite surface. Two kinds of images have been obtained: images showing aggregates of 16S ribosomal RNA molecules similar to those obtained from DNA solutions and others showing individual 16S ribosomal RNA molecules. An interesting characteristic of these images, recorded in constant current mode, is that the 16S ribosomal RNA molecules appear to be located below the graphite surface. The morphology and several structural parameters of the molecules were consistent with the data obtained from electron microscopy.     

A compact three-dimensional crystal form of the large ribosomal subunit from Bacillus stearothermophilus

A new form of well-ordered three-dimensional crystals of intact 50 S ribosomal subunits from Bacillus stearothermophilus have been obtained. Electron micrographs of positively stained sections of these crystals revealed that the ribosomal particles are packed closely. The cell parameters have been determined. Representative electron micrographs and their computed contoured filtered images are shown.     

Two-dimensional gel electrophoresis of ribosomal proteins from streptomycin-sensitive and streptomycin-resistant mutants of Chlamydomonas reinhardi.

Ribosomal proteins from three mutant strains of Chlamydomonas reinhardi were analysed and compared by one-dimensional and two-dimensional gel electrophoresis. One mutant was streptomycin-sensitive the other two were streptomycin-resistant, one with a Mendelian the other with a non-Mendelian pattern of inheritance. In the 30-S subunits of chloroplast ribosomes approximately 25 proteins are found and in the 50-S subunits 34 proteins. The 40-S subunits of cytoplasmic ribosomes contain about 31 proteins and the 60-S subunits 44 proteins. The molecular weights of most proteins in all subunits are in the range of 10 000 to 35 000. However, the 60-S subunits contain in addition a protein of molecular weight 50 000 and the 30-S subunits show 6-7 bands of molecular weights from 50 000 to 83 000. The proteins of the cytoplasmic 80-S ribosomes or of their subunits from all three mutants are electrophoretically identical. The proteins of the 70-S organellar ribosomes and both of their subunits show distinct differences between the three strains. Our results indicate that organellar ribosomal proteins are in part controlled by nuclear DNA and in part by organellar DNA.     

The molecular shape of dopamine beta-hydroxylase from chromaffin granules of bovine adrenal medulla

The structural features of the soluble dopamine beta-hydroxylase from chromaffin granules of bovine adrenal medulla were studied using negative staining and platinum shadowing electron microscopic methods. The enzyme was shown to be highly asymmetric as suggested in earlier hydrodynamic studies. The tetramer of the enzyme appeared as four subunits arranged in the shape of a planar rose with an estimated width of 15 nm. A minimum thickness of 3.0 nm for the enzyme monomer was calculated from the shadow length of unidirectionally shadowed molecules. A model composed of four oblate ellipsoid monomers in a tetrameric rose arrangement is proposed for the shape of the dopamine beta-hydroxylase molecule. Two monomers associate edge to edge to form an in-plane dimer and two dimers associate side-by-side with their respective long axes at a slight angle to form a tetramer. Theoretical calculations based on the model are consistent with previous hydrodynamic studies.