Electron microscopy and image processing applied to the study of protein structure and protein-protein interactions

The effects of physical exercise on the cigarette smoke-induced pulmonary oxidative response

Studies have shown that the oxidative power of cigarettes is related to the pathogenesis of several pulmonary diseases and that regular physical exercise contributes significantly to reducing the deleterious effects of cigarettes. The objective of the present study was to investigate the therapeutic effects of physical exercise on histological and oxidative stress markers in animals exposed to cigarette smoke. Thirty-six male, eight-week-old C57BL-6 mice were divided into four groups (n = 9 for each group): control, exercise, cigarette smoke, and cigarette smoke plus exercise. The cigarette smoke (CS) groups were exposed to cigarette smoke 3 times/day (4 cigarettes/session) for 60 consecutive days. The exercise groups were submitted to swimming physical training 5 days/week for eight weeks. Forty-eight hours after the last exercise and cigarette exposure, the animals were sacrificed using cervical traction. The right lung was removed, processed, and stored for future analysis. In addition to the analysis of collagen content (hydroxyproline), oxidant production (anion superoxide), antioxidant enzyme activity (SOD and CAT), and lipid and protein oxidative damage (TBARS and Carbonylation), histological and morphological studies were performed. The results revealed that the animals exposed to cigarette smoke showed enlargement and destruction of the alveolar septum and increases in the numbers of macrophages and neutrophils, as well as in the amount of collagen. Our results also showed a decrease in the volume density of elastic fibers and an increase in the volume density of airspaces. However, physical exercise partially improved these markers. Additionally, physical exercise decreased oxidant production and increased the activity of the enzymatic antioxidant defense system, but did not reverse lipid and protein oxidative damage induced by cigarette smoke. These results suggest that physical training partially improves histological and oxidative stress parameters in the lungs of animals chronically exposed to cigarette smoke and that other therapies can contribute to potentiate these effects.

Angular reconstitution: a posteriori assignment of projection directions for 3D reconstruction

In computerized tomography as well as in most problems of three-dimensional reconstruction from projections, one knows from the experimental set-up the angular relationships between the projections from which the reconstruction is to be calculated. A serious difficulty is encountered when the angles are not known. In this paper, a method of "angular reconstitution" is described, which allows the a posteriori determination of the relative angular orientations of the projections and thus enables the three-dimensional reconstruction of the object to be calculated. For asymmetric objects, a minimum of three projections is required, which should not be related by a tilt around a single rotation axis. The method can be applied to determine the three-dimensional structure of biological macromolecules based on electron micrographs of randomly oriented individual molecules. Angular reconstitution, in combination with multivariate statistical techniques to classify and average the characteristic views of a molecule forms a complete, self-contained methodology for molecular structure analysis by electron microscopy.

Structural analysis of F18 fimbriae expressed by porcine toxigenic Escherichia coli

The F18 fimbriae expressed by porcine toxigenic Escherichia coli strains are 1- to 2-mm-long filaments that mediate the adhesion of the bacteria to enterocytes. The backbone of these fimbriae is built from a major structural 15.1-kDa protein, FedA. The structure of isolated negatively stained F18 fimbriae imaged by dark-field scanning transmission electron microscopy (STEM) was resolved to approximately 2 nm. Analyzing their helical symmetry showed the axially repeating units to alternate in a "zigzag" manner around the helical axis with an axial rise of 2.2 nm. Two repeating units give rise to the observed 4.3-nm helical repeat, which is practically identical to the pitch of the one-start helix formed. Additionally, an axially repeating pattern with a 27-nm spacing was found on rotary-shadowed fimbriae. Mass-per-length determination of unstained F18 fimbriae by STEM revealed the axially repeating unit to have a molecular mass of 25.4 kDa, indicating that it is a FedA monomer, with the difference in mass arising from the minor subunits, FedE and FedF. The presence of the latter two proteins might cause the observed 27-nm axial pattern.

How to make tubular crystals by reconstitution of detergent-solubilized Ca2(+)-ATPase

In an attempt to better define the parameters governing reconstitution and two-dimensional crystallization of membrane proteins, we have studied Ca2(+)-ATPase from rabbit sarcoplasmic reticulum. This ion pump forms vanadate-induced crystals in its native membrane and has previously been reconstituted at high lipid-to-protein ratios for functional studies. We have characterized the reconstitution of purified Ca2(+)-ATPase at low lipid-to-protein ratios and discovered procedures that produce long, tubular crystals suitable for helical reconstruction. C12E8 (n-dodecyl-octaethylene-glycol monoether) was used to fully solubilize various mixtures of lipid and purified Ca2(+)-ATPase, and BioBeads were then used to remove the C12E8. Slow removal resulted in two populations of vesicles, and the proteoliposome population was separated from the liposome population on a sucrose density gradient. These proteoliposomes had a lipid-to-protein ratio of 1:2, and virtually 100% of molecules faced the outside of vesicles, as determined by fluorescein isothiocyanate labeling. Cycles of freeze-thaw caused considerable aggregation of these proteoliposomes, and, if phosphatidyl ethanolamine and phosphatidic acid were included, or if the bilayers were doped with small amounts of C12E8, vanadate-induced tubular crystals grew from the aggregates. Thus our procedure comprised two steps-reconstitution followed by crystallization-allowing us to consider mechanisms of bilayer formation separately from those of crystallization and tube formation.

The size, shape and stability of complement component C9

Electron microscopy of specimens of C9 tilted through 90 degrees visualized this protein to be a globular ellipsoid with dimensions of 77 x 70 x 52 A. To check the congruence of this observation with physical properties of the molecule, hydrodynamic parameters for C9 were determined. From this work a frictional ratio of 1.32 was calculated. C9 was compared with several other proteins of similar frictional ratios whose tertiary structures are known. All examples found of such proteins whose frictional ratios were between 1.26 and 1.37 are either heart-shaped or globular ellipsoids, but none are prolate ellipsoids. By comparison the size and shape of C9 determined by electron microscopy are congruent with its hydrodynamic parameters. Both electron microscopy and physical measurements suggest that the length (110-120 A) of C9 determined by neutron and X-ray scattering experiments is an overestimate. The source of the discrepancy was identified by the demonstration that the high concns of C9 employed in neutron and X-ray scattering work lead to aggregation of the protein. Thus, investigations involving neutron and X-ray scattering were measuring polydisperse solutions of C9. The deduced value of the radius of gyration from that work (33-35 A) is now recognized as being statistical and significantly higher than the correct value of monomeric C9 (26 A), which was calculated from electron microscopy measurements. Also high-resolution electron microscopy clearly visualized poly(C9) to be a barrel-stave construct. These results suggest that monomeric C9 must undergo a major conformational alteration to extend by 55-70 A in order to self-associate laterally in order to fashion the cylindrical poly(C9).

Has negative staining still a place in biomacromolecular electron microscopy?

Transmission electron microscopy of proteins has provided molecular- and in a few cases near-atomic-resolution structural information. In this review, we critically evaluate the potential and the limitations in obtaining molecular resolution, particularly with negatively stained specimens, and put these into perspective with cryomicroscopy of unstained frozen-hydrated and sugar-embedded preparations.

Physiological, morphological, and physicochemical characterization of a novel Escherichia coli bacteriophage, phage MM

A double-stranded DNA containing, T even-like, Escherichia coli bacteriophage, called MM, has been isolated from the local sewage and purified by polyethylene glycol precipitation followed by banding on a cesium chloride three-step gradient. It yields a burst size of 75 particles per infected cell, and has an adsorption coefficient of 3.3 x 10(-10) cm3/min and a latent period of 45 min. Electron microscopy of phage MM reveals an isometric icosahedral head, 92 nm long and 81 nm wide, and a 112-nm-long contractile tail with six pairs of 40-nm-long fibers attached to its baseplate. Phage MM appears similar to E. coli phage T4 or Salmonella phage O1. The density of phage MM in cesium chloride is 1.515 g/ml, and its total mass is 144 MDa. Gel electrophoresis of purified MM capsids displays two major capsid proteins in approximately equimolar amounts and with apparent molecular masses of 38 and 15 kDa. Similarly, purified MM tails yield two major polypeptides with apparent molecular masses of 55 and 16 kDa, most likely representing the major tail sheath and tail tube polypeptides. Its double-stranded DNA has a G-C content of 50%, a length of 131 kilobases (kb), and a mass of 89 MDa.

Glycolipid storage material in Fabry's disease: a study by electron microscopy, freeze-fracture, and digital image analysis

The glycolipid storage material in Fabry's disease was studied by electron microscopy of thin-sectioned (TS) and freeze-fractured (FF) specimens. In the kidney all deposits were found to be located in lysosomes, arranged as lamellar stacks. Deposits in the heart consisted of intracytoplasmic concentric whirls or folded lamellar structures. High resolution TS micrographs disclosed various defects in the lamellar structure. For stabilization, such defects require additional amphiphilic, surface-active molecules. These molecules could interact with other cellular constituents. The lamellar periodicity of the deposits in FF specimens was determined by reconstruction of the three-dimensional fracture face by digital image analysis. Homogeneous multilamellar deposits exhibited a periodicity of 14-15 nm, contrasting with the conventional estimates of 4-5 nm on TS micrographs. This difference is explained by better preservation of the physiologic hydrated state in FF specimens, with 1 vol of lipids binding 2 vol of water. Inhomogeneous structures with an even higher state of hydration included water lenses between the sheets. The strong hydration obviously contributes to the enlargement of the intracellular glycolipid deposits.

Crystallization of p68 on lipid monolayers and as three-dimensional single crystals

Two-dimensional crystals of p68, a Ca2+ -binding protein that has homology with members of the lipocortin/calpactin family, were obtained by interaction with a phospholipid monolayer. By measuring surface pressure at constant surface area, p68 was found to interact in a Ca2+ -dependent manner specifically with phosphatidylethanolamine, less so with phosphatidylserine and not at all with phosphatidylcholine. With dimyristoyl-phosphatidylethanolamine, two-dimensional crystalline arrays were formed. Image analysis of electron micrographs of these crystals, which diffracted to about 50 A, revealed p3 symmetry with a unit cell of about 178 A by 178 A; the protein densities showed a two-domain structure giving a cylindrical molecule of about 100 A by 35 A diameter packed as trimers. Three-dimensional microcrystals obtained without lipid or Ca2+ were suitable for electron microscopy and gave a tetragonal unit cell of about 256 A by 68 A. The implications of these observations on the structure and lipid specificity of p68 binding are discussed.

Computer image processing of electron micrographs of biological structures with helical symmetry

Methods are described for the analysis of electron micrographs of biological objects with helical symmetry and for the production of three-dimensional models of these structures using computer image reconstruction methods. Fourier-based processing of one- and two-dimensionally ordered planar arrays is described by way of introduction, before analysing the special properties of helices and their transforms. Conceiving helical objects as a sum of helical waves (analogous to the sum of planar waves used to describe a planar crystal) is shown to facilitate analysis and enable three-dimensional models to be produced, often from a single view of the object. The corresponding Fourier transform of such a sum of helical waves consists of a sum of Bessel function terms along layer lines. Special problems deriving from the overlapping along layer lines of terms of different Bessel order are discussed, and methods to separate these terms, based on analysing a number of different azimuthal views of the object by least squares, are described. Corrections to alleviate many technical and specimen-related problems are discussed in conjunction with a consideration of the computer methods used to actually process an image. A range of examples of helical objects, including viruses, microtubules, flagella, actin, and myosin filaments, are discussed to illustrate the range of problems that can be addressed by computer reconstruction methods.

Advances in image processing for electron microscopy: Part I

Methods are described for the analysis of electron micrographs of regular biological objects. Fourier-based processing of one-dimensionally ordered arrays is described by way of introduction, before analysing two-dimensional crystals in projection with the aim of enhancing signal:noise ratio and thus of feint features that were initially obscured. This form of analysis is then extended to decomposing the moiré patterns formed when sheets overlap, thereby enabling the separation of interfering image patterns. Analogous forms of an analysis can also be applied to objects with rotational symmetry. Methods for treating the effect of the microscope imaging system and compensating for lattice disorder in crystalline specimens are also discussed.

Crystalline tubes of myosin subfragment-2 showing the coiled-coil and molecular interaction geometry

We have produced crystalline tubes of chicken breast myosin long subfragment-2 that show order to resolutions better than 2 nm. The tubes were formed from a thin sheet in which the myosin long subfragment-2 molecules were arranged on an approximately rectangular crystalline lattice with a = 14.1 +/- 0.2 nm and b = 3.9 +/- 0.1 nm in projection. Shadowing indicated that the tube wall was approximately 7 nm thick and that the sheets from which it was formed followed a right-handed helix. Superposition of the lattices from the top and bottom of the tube produced a moire pattern in negatively stained material, but images of single sheets were easily obtained by computer image processing. Although several molecules were superimposed perpendicular to the plane of the sheet, the modulation in density due to the coiled-coil envelope was clear, indicating that the coiled-coils in these molecules were in register (or staggered by an even number of quarter pitches). In projection the coiled-coil had an apparent pitch of 14.1 nm (the axial repeat of the unit cell), but the small number of molecules (probably four) superimposed perpendicular to the plane of the sheet meant that pitches within approximately 1 nm of this value could have shown a modulation. Therefore, a more precise determination of the coiled-coil pitch must await determination of the sheet's three-dimensional structure. The coiled-coils of adjacent molecules within the plane of the sheet were staggered by an odd number of quarter pitches. This arrangement was similar to that between paramyosin molecules in molluscan thick filaments and may have features in common with other coiled-coil protein assemblies, such as intermediate filaments. Each molecule in the crystal had two types of neighbor: one staggered by an odd number of quarter pitches and the other by an even number of quarter pitches, as has been proposed for the general packing of coiled-coils (Longley, W., 1975, J. Mol. Biol., 93:111-115). We propose a model for the detailed packing within the sheet whereby molecules are inclined slightly to the plane of the sheet so that its thickness is determined by the molecular length.