Cryo-negative staining

Negative staining permits 4.0 A resolution with low-dose electron diffraction of catalase crystals

Low-dose electron diffraction of thin single crystals of catalase that are negatively stained with the light-atom compound, dipotassium glucose-1,6-diphosphate, reveals Bragg reflections extending to 4.0A (= 0.40 nm). Under the same conditions, negative staining with the traditional heavy-metal salt, ammonium molybdate, also gives diffraction spots extending to 4.0 A. These results establish that negative staining of protein crystals preserves periodic structural information into the high-resolution range, unlike the widely accepted current belief that this methodology can give a resolution limited to only 20-25 A.

Transmission electron microscopical studies on some haemolymph proteins from the marine polychaete Nereis virens

The hexagonal bilayer haemoglobin molecule from Nereis virens has been investigated in a comparative study using several different negative stain electron microscopical specimen preparations (i.e. by conventional adsorption to continuous carbon support films, by the negative staining-carbon film technique and by negative staining across the holes of holey carbon support films with air-drying and rapid freezing/cryo-negative staining). The benefits and limitations of these different approaches are indicated, with the overall conclusion that negative staining with ammonium molybdate across holes creates the best possibilities for molecular imaging, and also has the potential for the creation of two-dimensional (2D) crystals/arrays at the fluid-air interface. Of the different negative staining procedures presented, cryo-negative staining reveals the greatest details of N. virens haemoglobin. This is exemplified by the direct visualisation of the central linker-assembly within the haemoglobin molecule, a structural feature less clearly defined by the other negative staining techniques. A discoidal lipoprotein molecule (diameter 30-60nm; thickness ca 8nm) has been detected in N. virens, which represents the first documented account of an annelid haemolymph lipoprotein. The biological implications of this lipoprotein for lipid transport remain to be established. The presence of a low concentration of ferritin molecules in N. virens haemolymph is also shown, assisted by the formation of small 2D ferritin arrays in negatively stained specimens prepared across holes.

Structure analysis of soluble proteins using electron crystallography

Electron crystallography as a structural determination technique has grown dramatically in use over recent years. Improvements in microscopes, equipment, practical techniques, computation facilities and image processing methods are reflected in the increasing number of near-atomic resolution structures that have been published. In this review we shall summarize the techniques involved in structure determination of soluble proteins using electron crystallography. Many soluble protein structures have been investigated in this manner over the past two decades. Here we present several examples where a variety of approaches have been used to gradually increase the information obtained.

Comparison of the decameric structure of peroxiredoxin-II by transmission electron microscopy and X-ray crystallography

The decameric human erythrocyte protein torin is identical to the thiol-specific antioxidant protein-II (TSA-II), also termed peroxiredoxin-II (Prx-II). Single particle analysis from electron micrographs of Prx-II molecules homogeneously orientated across holes in the presence of a thin film of ammonium molybdate and trehalose has facilitated the production of a >/=20 A 3-D reconstruction by angular reconstitution that emphasises the D5 symmetry of the ring-like decamer. The X-ray structure for Prx-II was fitted into the transmission electron microscopic reconstruction by molecular replacement. The surface-rendered transmission electron microscopy (TEM) reconstruction correlates well with the solvent-excluded surface of the X-ray structure of the Prx-II molecule. This provides confirmation that transmission electron microscopy of negatively stained specimens, despite limited resolution, has the potential to reveal a valid representation of surface features of protein molecules. 2-D crystallisation of the Prx-II protein on mica as part of a TEM study resulted in the formation of a p2 crystal form with parallel linear arrays of stacked rings. This latter 2-D form correlates well with that observed from the 2.7 A X-ray structure of Prx-II solved from a new orthorhombic 3-D crystal form.

Light atom derivatives of structure-preserving sugars are unconventional negative stains

Although glucose and certain other sugars are known to greatly reduce distortion and denaturation of proteins during drying, use of this monosaccharide as an experimental negative stain does not permit imaging of lattice periodicities in test specimens of thin catalase crystals. However, the potassium and sodium salts of several forms of monophosphorylated glucose (200 mM), diphosphorylated glucose, monosulfated glucose, maltose-1-phosphate, and trehalose-6-phosphate, all dry into a glassy layer and scatter transmitted electrons sufficiently to show the 86 A major periods in catalase crystals. Glucose-6-phosphate provides sufficient image contrast at concentrations from 2 mM (=0.067%) to 500 mM (= 16.8%). Underfocusing increases visualization of the periodic lattice, indicating a large contribution of phase contrast to these images. Upon exposure to the electron beam, thicker regions of derivatized saccharides or pure glucose develop bubbling; this redistribution of dried stain largely can be precluded by imaging with low-dose exposures. Power spectra of images of catalase crystals contained within 200 mM disodium glucose-6-phosphate show that periodic information can be recorded to 21 A; some individual features of dipotassium glucose-6-phosphate distribution within the protein lattice have a measured width of around 5 A. The experimental results demonstrate that structure-preserving mono- and di-saccharides also serve successfully as negative stains after they are coupled to light atom scatterers.

Surface tongue-and-groove contours on lens MIP facilitate cell-to-cell adherence

The lens major intrinsic protein (MIP, AQP0) is known to function as a water and solute channel. However, MIP has also been reported to occur in close membrane contacts between lens fiber cells, indicating that it has adhesive properties in addition to its channel function. Using atomic force and cryo-electron microscopy we document that crystalline sheets reconstituted from purified ovine lens MIP mostly consisted of two layers. MIP lattices in the apposing membranes were in precise register, and determination of the membrane sidedness demonstrated that MIP molecules bound to each other via their extracellular surfaces. The surface structure of the latter was resolved to 0.61 nm and revealed two protruding domains providing a tight "tongue-and-groove" fit between apposing MIP molecules. Cryo-electron crystallography produced a projection map at 0.69 nm resolution with a mirror symmetry axis at 45 degrees to the lattice which was consistent with the double-layered nature of the reconstituted sheets. These data strongly suggest an adhesive function of MIP, and strengthen the view that MIP serves dual roles in the lens.

Self-assembly of beta-amyloid 42 is retarded by small molecular ligands at the stage of structural intermediates

Assemblyof the amyloid-beta peptide (Abeta) into fibrils and its deposition in distinct brain areas is considered responsible for the pathogenesis of Alzheimer's disease (AD). Thus, inhibition of fibril assembly is a potential strategy for therapeutic intervention. Electron cryomicroscopy was used to monitor the initial, native assembly structure of Abeta42. In addition to the known fibrillar intermediates, a nonfibrillar, polymeric sheet-like structure was identified. A temporary sequence of supramolecular structures was revealed with (i) polymeric Abeta42 sheets during the onset of assembly, inversely related to the appearance of (ii) fibril intermediates, which again are time-dependently replaced by (iii) mature fibrils. A cell-based primary screening assay was used to identify compounds that decrease Abeta42-induced toxicity. Hit compounds were further assayed for binding to Abeta42, radical scavenger activity, and their influence on the assembly structure of Abeta42. One compound, Ro 90-7501, was found to efficiently retard mature fibril formation, while extended polymeric Abeta42 sheets and fibrillar intermediates are accumulated. Ro 90-7501 may serve as a prototypic inhibitor for Abeta42 fibril formation and as a tool for studying the molecular mechanism of fibril assembly.

Unexpected property of trehalose as observed by cryo-electron microscopy

Trehalose is an agent useful in maintaining the integrity of many biological systems submitted to various stresses. It is also presumed to improve specimen preparation for electron microscopy and to reduce beam damage. Here we study the effect of trehalose on the preparation and observation by cryo-electron microscopy of thin vitrified films of biological suspensions. We observe that trehalose, as compared to sucrose, can indeed reduce electron beam damage to biological particles, as determined from the dose necessary for the onset of bubbling. Surprisingly, we also find that the contrast of biological particles is higher in a vitrified solution of trehalose than in one of sucrose. This effect can be explained if the water evaporation during the specimen preparation is less in the presence of trehalose than with sucrose, but we do not yet understand the underlying reasons since the evaporation properties of both sugars are similar at a macroscopic level. We conclude that trehalose is truly a remarkable substance and that more investigation is needed in order to fully understand its properties, and that the addition of ca. 3-5% trehalose to biological suspensions is a simple and useful method to reduce commonly arising drying artefacts and water evaporation in the thin film vitrification method.

Mitochondrial Lon of Saccharomyces cerevisiae is a ring-shaped protease with seven flexible subunits

Lon (or La) is a soluble, homooligomeric ATP-dependent protease. Mass determination and cryoelectron microscopy of pure mitochondrial Lon from Saccharomyces cerevisiae identify Lon as a flexible ring-shaped heptamer. In the presence of ATP or 5'-adenylylimidodiphosphate, most of the rings are symmetric and resemble other ATP-driven machines that mediate folding and degradation of proteins. In the absence of nucleotides, most of the rings are distorted, with two adjacent subunits forming leg-like protrusions. These results suggest that asymmetric conformational changes serve to power processive unfolding and translocation of substrates to the active site of the Lon protease.

A strategy for determining the orientations of refractory particles for reconstruction from cryo-electron micrographs with particular reference to round, smooth-surfaced, icosahedral viruses

Cryo-electron microscopy and three-dimensional image reconstruction are powerful tools for analyzing icosahedral virus capsids at resolutions that now extend below 1 nm. However, the validity of such density maps depends critically on correct identification of the viewing geometry of each particle in the data set. In some cases-for example, round capsids with low surface relief-it is difficult to identify orientations by conventional application of the two most widely used approaches-"common lines" and model-based iterative refinement. We describe here a strategy for determining the orientations of such refractory specimens. The key step is to determine reliable orientations for a base set of particles. For each particle, a list of candidate orientations is generated by common lines: correct orientations are then identified by computing a single-particle reconstruction for each candidate and then systematically matching their reprojections with the original images by visual criteria and cross-correlation analysis. This base set yields a first-generation reconstruction that is fed into the model-based procedure. This strategy has led to the structural determination of two viruses that, in our hands, resisted solution by other means.

Cholesterol-Streptolysin O Interaction: An EM Study of Wild-Type and Mutant Streptolysin O

We present transmission electron microscopical data from negatively stained specimens of cholesterol following interaction with the thiol-activated bacterial toxin streptolysin O (SLO) (wild-type and a number of cysteine substitution mutants), with and without chemical modification of the cysteine residues. Two experimental systems were used, one with an aqueous suspension of cholesterol microcrystals and the other with immobilized thin planar cholesterol crystals attached to a carbon film. In both systems the wild-type SLO and two cytolytically active mutants, Cys 530 --> Ala (C530A) and Ser 101 --> Cys (S101C), readily generated the characteristic SLO arc- and ring-like oligomers on the surface of cholesterol microcrystals and immobilized planar cholesterol crystals. An underlying array of bound toxin can sometimes be detected. In the presence of high concentrations of SLO monomer, extensive sheet-like networks of linked oligomers extend from the microcrystals. The SLO mutant Thr250 --> Cys (T250C), which also possesses a relatively high cytolytic activity, has been found to create ring-like toxin oligomers somewhat more slowly than wild-type SLO, but the linear monomolecular layer array of cholesterol-bound toxin is more readily detected. With mutant Asn402 --> Cys (N402C), which has approximately 10% cytolytic activity compared to wild-type SLO, the formation of ring-like oligomers is markedly reduced, with incomplete arcs and the parallel arrays predominating. Chemical modification of the functional cysteine groups of SLO mutants T250C and N402C completely inhibits the formation of toxin oligomers, but does not prevent the ability of these mutants to bind to cholesterol as a linear array. Such chemical modification is also known to abolish hemolysis/cytolysis. For both mutant T250C and N402C the parallel array of bound SLO adopts an orientation that appears to be determined by the underlying lattice of the crystalline cholesterol. The cholesterol-binding of biotinylated SLO mutant N402C was confirmed by labeling in suspension with 5-nm streptavidin-conjugated colloidal gold particles. Removal of the maltose-binding protein from the SLO fusion products increases the order of the monolayer array of biotinylated SLO bound to cholesterol crystals. Overall, our data support the concept that there is sterospecific binding of the SLO monomer to crystalline cholesterol bilayers, prior to oligomer formation. With the mutants tested, cysteine modification does not prevent binding to cholesterol, but subsequent release and oligomer formation are blocked. Copyright 1998 Academic Press.