Electron microscopic analysis of tropomyosin paracrystals.

Negatively stained images of divalent cation-induced tropomyosin paracrystals show polymorphic patterns which are almost bipolar. Although these bipolar forms are naturally due to antiparallel arrays of molecules, the precise molecular arrangements have not been clarified yet except in the case of one type of these polymorphic paracrystals by Stewart and McLachlan [(1976) J. Mol. Biol. 103, 251--269]. In the previous paper we showed that the lead-induced polar paracrystal is a parallel and in-register array of tropomyosin molecules. Moreover, we have made it possible to locate a given residue on the staining pattern. By overlapping two photographic transparencies of the polar paracrystal antiparallel, directly observed images of polymorphic bipolar paracrystals could be synthesized photographically with fidelity. The overlap length between N-terminals of antiparallel pairs of molecules could be easily determined without any assumptions. Next, we considered the stabilizing forces involved in the morphogenesis of such polymorphic paracrystals. The cation-bridged attractive forces already proposed by some groups were insufficient to account for the stability of some specific forms of tropomyosin paracrystals. From the primary amino acid sequence of tropomyosin, we calculated the changes of repulsive forces between the basic residues with changes of molecular overlap length between the N-terminals of antiparallel pairs. By setting the values of charge appropriately, we could account well for the stability of the polymorphic structures observed by electron microscopy.     

The axial repeats in paracrystals of light meromyosin and its complex with C-protein

We examined the axial repeats in electron micrographs of three types of negatively stained paracrystals (two tactoid- and one sheet-like type) of rabbit light meromyosin (LMM) and its complex with C-protein characterized previously by similar axial period of about 43.0 nm. Assuming for the axial repeat in type II tactoids the value of 42.93 +/- 0.05 nm as it was determined by X-ray diffraction technique (Yagi and Offer 1981), we found average axial repeats in type I tactoid and in sheet-like paracrystal of 42.93 +/- 0.75 nm and 43.50 +/- 0.62 nm respectively. Analyzing the micrographs where the two types paracrystals are located side-by-side we determined rather accurately the average ratio of axial repeat in sheet-like paracrystal to that in type I tactoid (1.013 +/- 0.002). Taking 42.93 nm as the axial repeat in type I tactoid, the axial repeat in sheet-like paracrystal was found to be 43.50 +/- 0.08 nm. C-protein binds to LMM with the period of the underlying LMM paracrystals and independently of the value of their axial repeats. Two different axial repeats (42.9 nm and 43.5 nm) revealed for LMM paracrystals in this study precisely coincide with the average repeat periods of myosin crossbridges along the thick filaments found for different physiological states of skeletal muscles (Lednev and Kornev 1987). Molecular basis for the appearance of two structural states in LMM paracrystals and in the shafts of thick filaments are discussed.     

Light meromyosin paracrystal formation

Studies of paracrystal formation by column purified light meromyosin (LMM) prepared in a variety of ways led to the following conclusions: (a) different portions of the myosin rod may be coded for different stagger relationships. This was concluded from observations that paracrystals with different axial repeat periodicities could be obtained either with LMM framents of different lengths prepared with the same enzyme, or with LMM fragments of identical lengths but prepared with different enzymes. (b) Paracrystals with a 14-nm axial repeat periodicity are most likely formed by the aggregation of sheets with a 44-nm axial repeat within the sheets which are staggered by 14 nm. All of the axial repeat patterns expected from one sheet or aggregates of more than one sheet, on this basis, were observed in the same electron micrograph. (c) C-protein binding probably occurs preferentially to LMM molecules related in some specific way. This was concluded from the observation that the same axial repeat pattern was obtained in paracrystals formed from different LMM preparations in the presence of C-protein, regardless of differences in the axial repeat obtained in the absence of C-protein. (d) Nucleic acid is responsible for the 43-nm axial repeat patterns observed in paracrystals formed by the ethanol-resistant fraction of LMM. In the absence of nuclei acid, paracrystals with a 14nm axial repeat are obtained. (e) The 43-nm axial repeat pattern observed with the ethanol-resistant fraction of LMM is different for LMM preparations obtained by trypsin and papain digestions.     

Molecular interactions in paracrystals of a fragment corresponding to the alpha-helical coiled-coil rod portion of glial fibrillary acidic protein: evidence for an antiparallel packing of molecules and polymorphism related to intermediate filament structure

We have expressed in Escherichia coli a fragment of c-DNA that broadly corresponds to the alpha-helical coiled-coil rod section of glial fibrillary acidic protein (GFAP) and have used the resultant protein to prepare paracrystals in which molecular interactions can be investigated. An engineered fragment of mouse GFAP c-DNA was inserted into a modified version of the E. coli expression vector pLcII, from which large quantities of a lambda cII-GFAP rod fusion protein were prepared. A protein fragment corresponding to the GFAP rod was then obtained by proteolysis with thrombin. Paracrystals of this material were produced using divalent cations (Mg, Ca, Ba) in the presence of a chaotrophic agent such as thiocyanate. These paracrystals showed a number of polymorphic patterns that were based on a fundamental pattern that had dyad symmetry and an axial repeat of 57 nm. Analysis of both positive and negative staining patterns showed that this fundamental pattern was consistent with a unit cell containing two 48-nm-long molecules in an antiparallel arrangement with their NH2 termini overlapping by approximately 34 nm. More complicated patterns were produced by stacking the fundamental pattern with staggers of approximately 1/5, 2/5, and 1/2 the axial repeat. The molecular packing the unit cell was consistent with a range of solution studies on intermediate filaments that have indicated that a molecular dimer (i.e., a tetramer containing four chains or two coiled-coil molecules) is an intermediate in filament assembly. Moreover, these paracrystals allow the molecular interactions involved in the tetramer to be investigated in some detail.     

Effect of H-protein on the formation of myosin filaments and light meromyosin paracrystals

H-protein is a component of the thick filaments of skeletal myofibrils. Its effects on the assembly of myosin into filaments and on the formation of light meromyosin (LMM) paracrystals at low ionic strength have been investigated. H-protein reduced the turbidities of myosin filament and LMM paracrystal suspensions. Electron microscopic observation showed that the appearances of the filaments prepared in the presence and absence of H-protein were different. The filament length was not substantially changed by H-protein, but the diameter of the myosin filament was markedly reduced. H-protein bound to LMM and co-sedimented with it at low ionic strength upon centrifugation. Two types of paracrystals, spindle-shaped and sheet-like, were observed in LMM suspensions. H-protein altered the structure of the LMM paracrystals, especially the spindle-shaped ones. The thickness of the spindle-shaped paracrystals was reduced when H-protein was present during LMM paracrystal formation. On the other hand, periodic features along the long axis of the sheet-like paracrystals were retained even at high ratios of H-protein to LMM. However, there were fewer sheet-like paracrystals in the LMM suspensions containing H-protein than in the control. These results suggest that H-protein interferes with self-association of myosin molecule into filaments due to its binding to the tail portion of the myosin. However, H-protein does not have a length-determining effect on the formation of myosin filaments.     

X-ray diffraction and electron microscopy of a light meromyosin tactoid

The structure of a tactoid of light meromyosin with a 43-nm periodicity was studied by both X-ray diffraction and electron microscopy. Such tactoids were formed from light meromyosin prepared by a short tryptic digestion (5 min) of myosin.A strong magnetic field (6 kgauss) was employed to obtain oriented specimens of tactoids for X-ray diffraction. The oriented tactoids gave equatorial reflections from a rectangular lattice with a unit cell of 6·5 nm × 3·9 nm (at pH 6·6) in a plane perpendicular to the long axis of the tactoid. This lattice shrank anisotropically when the pH was lowered. The meridional reflections could be indexed as orders of 42·93 ± 0·05 nm.The tactoids were frequently associated with sheet-like structures termed banded sheets. In negative stain these banded sheets showed the same band pattern as the tactoids with 10 nm wide light and 33 nm wide dark bands. However, in thin banded sheets the density of neighbouring dark bands alternated so that the true axial repeat was 86 nm. Optical diffraction showed that the face-on view of the banded sheet had a unit cell of 3·6 nm × 86 nm.From these observations a plausible model for the structure of the light meromyosin tactoid has been deduced. In this model the tactoid is made by a stacking of unit layers. A unit cell (6·5 nm × 3·9 nm × 86 nm) contains four light meromyosin molecules, each 90 nm long and packed co-planar, not all of which are in an identical environment. The molecules make parallel interactions with staggers of 86 and 43 nm and antiparallel interactions with overlaps of 84 and 41 nm.     

Structure of magnesium paracrystals of α-tropomyosin

The molecular packing of magnesium paracrystals of α-tropomyosin has been examined by electron microscopy. Previous work (Caspar et al., 1969) had shown that these structures are composed of antiparallel arrays of molecules and we have now studied the relative positions of the molecules by matching the banding patterns of paracrystals positively stained with uranyl acetate to the sequence of the molecule. The overlap between the C-termini of the molecules in the unit cell is 175 ± 2 residues and the overlap of the N-termini lies in the range 107 to 122 residues. In the long overlap region (between C-termini), and probably also in the short overlap region, the molecular packing is such that the periodic zones of negative charge present in the sequence (Stewart & McLachlan, 1975) lie opposite one another. We propose that magnesium bridges between opposing negative charges contribute strongly to the stability of the structure. We confirm earlier work (Stewart, 1975b) on the absolute orientation of the molecules in the paracrystal: the troponin binding site on tropomyosin is approximately 130 Å from the C-terminus, and Cys190 is within 10 to 15 Å units of the C-C dyad.     

Structure of α-tropomyosin magnesium paracrystals: II. Simulation of staining patterns from the sequence and some observations on the mechanism of positive staining

Electron micrographs of magnesium paracrystals of α-tropomyosin stained with uranyl acetate show a repeating pattern of 14 dark bands. Previous studies (Caspar et al., 1969; Ohtsuki, 1974) have shown that the molecules in the paracrystal lie antiparallel with their ends near two prominent white bands. These white lines divide the pattern into two zones containing nine and five dark bands, respectively, with the longer zone corresponding to the overlap between C termini. The present study shows that the intensity of the prominent white lines is reduced after digesting tropomyosin with carboxypeptidase A. This implies that, even in supposedly positively stained material, the white lines result from the exclusion of residual negative stain by the local thickening associated with the overlap of the ends of consecutive parallel molecules (NC overlap). Computer image processing and least-squares analysis have been employed to relate the positively stained patterns observed in both digested and undigested material to molecular positions and the amino acid sequence. Over a range of different staining criteria, it is shown that the pattern is fitted best when the C termini overlap by 176 ± 5 residues and the ends of consecutive parallel molecules overlap by 11 ± 5 residues. Uranyl ions appear to bind to carboxyl groups in the structure unless they form salt bridges with basic residues or they lie in the innermost positions of the tropomyosin coiled coil. Systematic differences between predicted and observed patterns near the molecular ends suggest that the conformation of the NC overlap may not be completely α-helical. A model with a globular N terminus and an extended C terminus is more consistent with the observed staining patterns and also offers an explanation for some other observations.     

Interaction of aldolase with actin-containing filaments. Structural studies.

Electron micrographs of the paracrystals formed when fructose bisphosphate aldolase (EC 4.1.2.13) is added to actin-containing filaments were analysed by computer methods so that ultrastructural changes could be correlated with the various stoicheiometries of binding determined in the preceding paper [Walsh, Winzor, Clarke, Masters & Morton (1980) Biochem. J. 186, 89-98]. Paracrystals formed with aldolase and either F-actin or F-actin-tropomyosin have a single light transverse band every 38 nm, which is due to aldolase molecules cross-linking the filaments. In contrast, the paracrystals formed between aldolase and F-actin-tropomyosin-troponin filaments show two transverse bands every 38 nm: a major band, interpreted as aldolase binding to troponin, and a minor band, interpreted as aldolase cross-linking the filaments. The intensity of the minor band varies with Ca2+ concentration, being greatest when the Ca2+ concentration is low. A model for the different paracrystal structures which relates the various patterns and binding stoicheiometries to structural changes in the actin-containing filaments is proposed.     

The myosin filament. XIII. The sensitivity of LMM assembly to Mg.ATP

An LMM fragment (Mr 62,000) of myosin has been prepared which has aggregation properties that are sensitive to the presence of Mg.ATP. Aggregation of the LMM by reducing the ionic strength in the presence of 1 mM Mg.ATP produces non-periodic aggregates which gradually rearrange to paracrystals with a 43 nm axial repeat pattern. This fragment includes the C-terminal end of the myosin rod starting at residue 1376. Therefore, at least one of the Mg.ATP binding sites responsible for this effect is located somewhere along this region of the myosin rod. Although assembly of the rod fragment of myosin into paracrystals does not show sensitivity to Mg.ATP, assembly of intact myosin molecules to form filaments does show sensitivity to Mg.ATP. For myosin filaments, assembly initially gives a broad distribution around a mean length of 1.5 microns, which sharpens around the mean length with time. The rearrangement of the LMM rods and intact myosin molecules both induced by the presence of Mg.ATP are probably related. These findings highlight the complexity of the cooperative interactions between different portions of the myosin molecule that are involved in determining the assembly properties of the intact molecule.     

Orientation of skeletal muscle actin in strong magnetic fields

Measurement of birefringence is used to follow actin filament and paracrystal formation in a strong magnetic field. Both F-actin and paracrystals orientate parallel to the field. This confirms that globular proteins arranged in filamentous assemblies can orientate in magnetic fields. This is consistent with the alpha-helical component of the actin subunits being approximately aligned along the actin filament.     

Three-dimensional reconstruction of thick filaments from Limulus and scorpion muscle

We have produced three dimensional reconstructions, at a nominal resolution of 5 nm, of thick filaments from scorpion and Limulus skeletal muscle, both of which have a right-handed four-stranded helical arrangement of projecting subunits. In both reconstructions there was a distinct division of density within projecting subunits consistent with the presence of two myosin heads. Individual myosin heads appeared to be curved, with approximate dimensions of 16 X 5 X 5 nm and seemed more massive at one end. Our reconstructions were consistent with the two heads in a projecting subunit being arranged either antiparallel or parallel to each other and directed away from the bare zone. Although we cannot exclude the second of these interpretations, we favor the first as being more consistent with both filament models and also because it would enable easy phosphorylation of light chains. The antiparallel interpretation requires that the two heads within a subunit derive from different myosin molecules. In either interpretation, the two heads have different orientations relative to the thick filament shaft.     

Mg2+-paracrystal formation of tropomyosin as a condensation phenomenon. Effects of pH, salt, temperature, and troponin binding.

Tropomyosin (Tm) paracrystal formation induced by Mg2+ was studied by monitoring increases in light scattering. Paracrystals formed above a critical Tm concentration with lag phases in the time courses at pH 7.5 and 6.0, indicating that condensation polymerization processes are involved. The kinetic data at pH 7.5 reasonably fit a model in which nucleation and elongation are taken into account. The rate and extent of light scattering increased at low [Mg2+] and decreased at high [Mg2+] with a maximum at [Mg2+] = 15 mM, indicating different effects of Mg2+ in the two [Mg2+] ranges. The paracrystals were destabilized by increasing the salt concentration and decreasing the temperature. Mg2+ produces paracrystals at pH 6.0 and pH 7.5 by different kinetic mechanisms. Different Tm intermolecular interactions at the two pH values were indicated by studies of the excimer fluorescence of pyrene-labeled Tm and by effects of salt and temperature on the kinetics. At pH 6.0 Tm more readily formed paracrystals with decreased electrostatic effects. Effects of troponin on Mg2+-paracrystal formation of Tm at the two pH values correlated with the known differences in paracrystal structure when troponin is bound to Tm.     

Prismatic cristae and paracrystalline inclusions in mitochondria of myocardial cells of the oyster Crassostrea virginica Gmelin

Summary Several types of unusual mitochondrial configurations were found in myocardial cells of the oyster Crassostrea virginica Gmelin. These mitochondria include, in order of frequency, prismatic cristae, filamentous paracrystals in honeycomb and herringbone configurations, and paracrystals composed of rows of electron dense particles. The long, parallel, evenly spaced prismatic cristae are square or rhomboidal in cross section. In the space between the prismatic cristae are rodlike structures (4–6 nm in diameter) that are regularly spaced about 12nm apart and appear to pass between adjacent cristae. Filamentous paracrystals are observed in slender, elongated mitochondria. The filament spacing and form of these paracrystals suggest that they are composed of the intercristal rods. Alternatively, filamentous paracrystals might be tangential sections of prismatic cristae and intercristal rods. Particulate paracrystals which consist of dense lines or rows of particles are the least frequent type of unusual configuration. The particles are triangular, possibly pyramidal, in shape; their bases are 10–12 nm thick and repeat in rows every 17–18 nm. There is a close association between particulate paracrystals and prismatic cristae plus intercristal rods. Although similar mitochondrial configurations have been associated with disease or altered metabolism in a number of species, we have found no such association in the oyster as yet.Supported in part by the Mississippi-Alabama Sea Grant Consortium, through NOAA, Dept. of Commerce under grant no. NA 79AA-D-0049We wish to thank Ms. Barbara M. Hyde, Ms. Patricia A. Vermiere and Mr. Robert Allen for their technical assistance     

Helical disorder and the filament structure of F-actin are elucidated by the angle-layered aggregate

Angle-layered aggregates of F-actin are net-like structures induced by Mg2+ concentrations below that used to form paracrystals. These aggregates incorporate the angular disorder of subunits, which has been described elsewhere for isolated actin filaments. Because this disorder is incorporated into the aggregates in solution at the time they are formed, the possibility of negative stain preparation being responsible for the disorder is excluded. The simple two-layered geometry of the angle-layered aggregate provides information about the shape of the component actin filaments free from the superposition of large numbers of layers. A model for the filament shape, derived from single filaments and confirmed by the angle-layered aggregate, is different from those that have previously emerged from paracrystal studies. An understanding of the interfilament bond in both the angle-layered aggregate and the paracrystal allows one to reconcile these different models. We have found a bipolar bonding rule, with staggered crossover points in the angle-layered aggregate, which we suggest is also responsible for Mg2+ paracrystals. This bonding rule can explain the apparent alignment of crossover points in adjacent filaments in paracrystals as a consequence of the superposition of staggered filaments.     

Crystal structure of an extended-conformation leucine-enkephalin dimer monohydrate

The structure of a new crystal form of leucine-enkephalin has been determined by X-ray diffraction. There are two independent molecules in the asymmetric unit and both have extended peptide backbone conformations with side-chains arranged alternately above and below the backbone planes. The two pentapeptides are hydrogen-bonded to each other and to other molecules forming an extended antiparallel beta-pleated sheet. The structure differs from that in similar crystals of methionine enkephalin primarily in side-chain orientations and inter-sheet interactions.     

Simulation Studies on the Stabilities of Aggregates Formed by Fibril-Forming Segments of α-Synuclein

Abstract

We performed molecular dynamics simulations for various oligomers with different β-sheet conformations consisting of α-Synuclein 71–82 residues using an all atom force field and explicit water model. Tetramers of antiparallel β-sheet are shown to be stable, whereas parallel sheets are highly unstable due to the repulsive interactions between bulky and polar side chains as well as the weaker backbone hydrogen bonds. We also investigated the stabilities of double antiparallel β-sheets stacked with asymmetric and symmetric geometries. Our results show that this 12 amino acid residue peptide can form stable β-sheet conformers at 320K and higher temperatures. The backbone hydrogen bonds in β-sheet and the steric packing between hydrophobic side chains between β-sheets are shown to give conformational stabilities.     

A study on the structure of paracrystals of F-actin.

The structure of three types of paracrystals formed by a muscle protein, actin, was studied by electron microscopy using the technique of optical diffraction and filtering methods.The type I paracrystal of F-actin⁴ had a flat net structure and each thread of the net appeared to be made of a single double-stranded filament of F-actin. Its unit cell was rhombic with sides of about 340 Å in length. The narrower angle of the rhomb was about 30 °. A side of the rhomb corresponded to one repeating unit of F-actin. The cross-connecting point of the net appeared to occur at a cross-over point of the double helical F-actin filament when the paracrystal plane was observed perpendicularly. A set of parallel filaments running in one direction seem to simply overlie another set of parallel filaments running in another direction.The type II paracrystal also had a flat net structure with a unit cell of the same size and shape as type I, but had twice the amount of material in the unit cell in comparison with that of type I; a thread of type II was made of a pair of F-actin filaments. The type II paracrystal seemed to be made by attaching the F-actin filaments side-by-side to filaments of the type I paracrystal. These newly associated filaments cross-connected with each other in the same manner as those of the type I paracrystal.The type III paracrystal was a side-by-side aggregate of F-actin filaments. There was no lateral order between the neighbouring filaments.     

Dependence of thick filament structure in relaxed mammalian skeletal muscle on temperature and interfilament spacing

Contraction of skeletal muscle is regulated by structural changes in both actin-containing thin filaments and myosin-containing thick filaments, but myosin-based regulation is unlikely to be preserved after thick filament isolation, and its structural basis remains poorly characterized. Here, we describe the periodic features of the thick filament structure in situ by high-resolution small-angle x-ray diffraction and interference. We used both relaxed demembranated fibers and resting intact muscle preparations to assess whether thick filament regulation is preserved in demembranated fibers, which have been widely used for previous studies. We show that the thick filaments in both preparations exhibit two closely spaced axial periodicities, 43.1 nm and 45.5 nm, at near-physiological temperature. The shorter periodicity matches that of the myosin helix, and x-ray interference between the two arrays of myosin in the bipolar filament shows that all zones of the filament follow this periodicity. The 45.5-nm repeat has no helical component and originates from myosin layers closer to the filament midpoint associated with the titin super-repeat in that region. Cooling relaxed or resting muscle, which partially mimics the effects of calcium activation on thick filament structure, disrupts the helical order of the myosin motors, and they move out from the filament backbone. Compression of the filament lattice of demembranated fibers by 5% Dextran, which restores interfilament spacing to that in intact muscle, stabilizes the higher-temperature structure. The axial periodicity of the filament backbone increases on cooling, but in lattice-compressed fibers the periodicity of the myosin heads does not follow the extension of the backbone. Thick filament structure in lattice-compressed demembranated fibers at near-physiological temperature is similar to that in intact resting muscle, suggesting that the native structure of the thick filament is largely preserved after demembranation in these conditions, although not in the conditions used for most previous studies with this preparation.     

Instability of pleomorphic tubulin paracrystals artificially induced by Vinca alkaloids in tissue-cultured cells

The processes of tubulin paracrystal induction in Chinese hamster ovary cells treated with a Vinca alkaloid, ie, vinblastine or vincristine, and treated simultaneously with one of the Vinca alkaloids and colcemid or colchicine were followed by four different microscopic techniques, in particular by tubulin-immunofluorescence. Vinca alkaloid alone, in lower concentrations, induced basically tactoid or needle-shaped (N-shaped) paracrystals. However, the formation of crystalloid was greatly enhanced by increasing the concentration of Vinca alkaloid. Square or barrel-shaped (S-shaped) and hexagonal paracrystals were also commonly induced by simultaneous treatment with a Vinca alkaloid and colcemid or colchicine. Large rectangular paracrystals often displayed fibrillar or lamellar fine structures which ran perpendicular to the long axis but tended to cleave into fragments by spontaneous splitting. Electron micrographs revealed the fine structure of crystalloids to be aggregates of numerous filaments. The growth of paracrystals, particularly N-shaped crystals, was markedly inhibited when cells were exposed to drug(s) at a low temperature (4 degrees C). We confirmed that both N- and S-shaped paracrystals dissociated rapidly after the culture medium was replaced with fresh, drug-free medium. Glutaraldehyde-fixed paracrystals treated with RNase solution were stained with acridine orange, showing a weak orange color. Possible factors involved in the assembly and disassembly of tubulin paracrystals are discussed.