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

Cryo-transmission electron microscopy structure of a gigadalton peptide fiber of de novo design

Nature presents various protein fibers that bridge the nanometer to micrometer regimes. These structures provide inspiration for the de novo design of biomimetic assemblies, both to address difficulties in studying and understanding natural systems, and to provide routes to new biomaterials with potential applications in nanotechnology and medicine. We have designed a self-assembling fiber system, the SAFs, in which two small α-helical peptides are programmed to form a dimeric coiled coil and assemble in a controlled manner. The resulting fibers are tens of nm wide and tens of μm long, and, therefore, comprise millions of peptides to give gigadalton supramolecular structures. Here, we describe the structure of the SAFs determined to approximately 8 Å resolution using cryotransmission electron microscopy. Individual micrographs show clear ultrastructure that allowed direct interpretation of the packing of individual α-helices within the fibers, and the construction of a 3D electron density map. Furthermore, a model was derived using the cryotransmission electron microscopy data and side chains taken from a 2.3 Å X-ray crystal structure of a peptide building block incapable of forming fibers. This was validated using single-particle analysis techniques, and was stable in prolonged molecular-dynamics simulation, confirming its structural viability. The level of self-assembly and self-organization in the SAFs is unprecedented for a designed peptide-based material, particularly for a system of considerably reduced complexity compared with natural proteins. This structural insight is a unique high-resolution description of how α-helical fibrils pack into larger protein fibers, and provides a basis for the design and engineering of future biomaterials.

Structures of smooth muscle myosin and heavy meromyosin in the folded, shutdown state

Remodelling the contractile apparatus within smooth muscle cells allows effective contractile activity over a wide range of cell lengths. Thick filaments may be redistributed via depolymerisation into inactive myosin monomers that have been detected in vitro, in which the long tail has a folded conformation. Using negative stain electron microscopy of individual folded myosin molecules from turkey gizzard smooth muscle, we show that they are more compact than previously described, with heads and the three segments of the folded tail closely packed. Heavy meromyosin (HMM), which lacks two-thirds of the tail, closely resembles the equivalent parts of whole myosin. Image processing reveals a characteristic head region morphology for both HMM and myosin, with features identifiable by comparison with less compact molecules. The two heads associate asymmetrically: the tip of one motor domain touches the base of the other, resembling the blocked and free heads of this HMM when it forms 2D crystals on lipid monolayers. The tail of HMM lies between the heads, contacting the blocked motor domain, unlike in the 2D crystal. The tail of whole myosin is bent sharply and consistently close to residues 1175 and 1535. The first bend position correlates with a skip in the coiled coil sequence, the second does not. Tail segments 2 and 3 associate only with the blocked head, such that the second bend is near the C-lobe of the blocked head regulatory light chain. Quantitative analysis of tail flexibility shows that the single coiled coil of HMM has an apparent Young's modulus of about 0.5 GPa. The folded tail of the whole myosin is less flexible, indicating interactions between the segments. The folded tail does not modify the compact head arrangement but stabilises it, indicating a structural mechanism for the very low ATPase activity of the folded molecule.

Engineering nanoscale order into a designed protein fiber

We have established a designed system comprising two peptides that coassemble to form long, thickened protein fibers in water. This system can be rationally engineered to alter fiber assembly, stability, and morphology. Here, we show that rational mutations to our original peptide designs lead to structures with a remarkable level of order on the nanoscale that mimics certain natural fibrous assemblies. In the engineered system, the peptides assemble into two-stranded alpha-helical coiled-coil rods, which pack in axial register in a 3D hexagonal lattice of size 1.824 nm, and with a periodicity of 4.2 nm along the fiber axis. This model is supported by both electron microscopy and x-ray diffraction. Specifically, the fibers display surface striations separated by nanoscale distances that precisely match the 4.2-nm length expected for peptides configured as alpha-helices as designed. These patterns extend unbroken across the widths (>/=50 nm) and lengths (>10 microm) of the fibers. Furthermore, the spacing of the striations can be altered predictably by changing the length of the peptides. These features reflect a high level of internal order within the fibers introduced by the peptide-design process. To our knowledge, this exceptional order, and its persistence along and across the fibers, is unique in a biomimetic system. This work represents a step toward rational bottom-up assembly of nanostructured fibrous biomaterials for potential applications in synthetic biology and nanobiotechnology.

Skip residues and charge interactions in myosin II coiled-coils: implications for molecular packing

Molecular packing of myosin II coiled-coil rods into myosin filaments and the role of skip residues in the heptad sequence have been investigated. Sequence comparison of rods from skeletal, smooth and non-muscle myosin II shows that different myosin II subtypes have significantly different charge distributions. Analysis of the ionic interactions between adjacent rods with changing molecular overlap relates the different patterns of charge to the different structures of skeletal and smooth muscle myosin II filaments. It is shown in the case of skeletal muscle myosin II that the skip residues have a critical role in keeping these unique patterns of charge in perfect phase. Only one of the previously suggested packing models for myosin II filaments, with a slight modification, is supported, since it satisfies all the sequence-predicted axial shifts between adjacent rods. Such analysis significantly advances understanding of myosin filament assembly properties and will help to provide a basis for the proper understanding of myosin-associated diseases.

Assembly of Acanthamoeba Myosin-II Minifilaments. Model of Anti-parallel Dimers Based on EM and X-ray Diffraction of 2D and 3D Crystals

Current models suggest that the first step in the assembly of Acanthamoeba myosin-II is anti-parallel dimerization of the coiled-coil tails with an overlap of 15 nm. Sedimentation equilibrium experiments showed that a construct containing the last 15 heptads and the non-helical tailpiece of the myosin-II tail (15T) forms dimers. To examine the structure of the 15T dimer, we grew 3D and 2D crystals suitable for X-ray diffraction and electron image analysis, respectively. For both conditions, crystals formed in related space and plane groups with similar unit cells (a=87.7 A, b=64.8 A, c=114.9 A, beta=108.0 degrees). Inspection of the X-ray diffraction pattern and molecular replacement analysis revealed the orientation of the coiled-coils in the unit cell. A 3D density map at 15A in-plane resolution derived from a tilt series of electron micrographs established the solvent content of the 3D crystals (75%, v/v), placed the coiled-coil molecules at the approximate translation in the unit cell, and revealed the symmetry relationships between molecules. On the basis of the low-resolution 3D structure, biochemical constraints, and X-ray diffraction data, we propose a model for myosin interactions in the anti-parallel dimer of coiled-coils that guide the first step of myosin-II assembly.

The kinase activity of the giant protein projectin of the flight muscle of Locusta migratoria

Projectin is a member of the functionally and structurally heterogeneous family of myosin light chain kinases associated to myosin of synchronous as well as asynchronous insect muscles. We examined the phosphotransferase activity of projectin from flight muscle of Locusta migratoria. Isolated projectin exhibits an unstimulated autophosphorylation activity in vitro. We observed differences in the formation of synthetic filaments with myosin, and paramyosin depending on if projectin was autophosphorylated in vitro or not. Aggregates of native projectin with myosin and paramyosin (molar ratio 0.08:1:0.5) showed diameters 20-50 nm similar to those of myosin filaments. When in vitro autophosphorylated projectin was used we predominantly obtained, however, subfilament-like structures of only 7-10 nm in diameter. The in vitro autophosphorylation of projectin was suppressed in the presence of either acto-myosin, actin-filaments or myosin, but still seems to exhibit a phosphorylation activity: Projectin added to actomyosin resulted in the phosphorylation of three polypeptides of apparent molecular masses of 200, 165 and 100 kDa, respectively. These data suggest that the autophosphorylation activity of projectin is regulated by its environment. We conclude, therefore, a dual function of its kinase domain: at first, a role of its autophosphorylation in the formation of myosin filaments (association of subfilaments to filaments); secondly, the transphosphorylation activity of projectin modulates the contractile response of the actomyosin system by phosphorylating some of its components. Moreover, we could stimulate in vitro the projectin autophosphorylation 3.4-fold by calmodulin (EC50 = 17.8 nM). However, the transphosphorylations described above were not stimulated by calmodulin.

A role for C-protein in the regulation of contraction and intracellular Ca2+ in intact rat ventricular myocytes

1. C-protein is a major component of muscle thick filaments whose function is unknown. We have examined for the first time the role of the regulatory binding domain of C-protein in modulating contraction and intracellular Ca2+ concentration ([Ca2+]i) in intact cardiac myocytes. 2. Rat ventricular myocytes were reversibly permeabilised with the pore-forming toxin streptolysin O. Myosin S2 (which binds to the regulatory domain of C-protein) was introduced into cells during permeabilisation to compete with the endogenous C-protein-thick filament interaction. 3. Introduction of S2 into myocytes increased contractility by approximately 30%, significantly lengthened the time to peak of the contraction and the time to half-relaxation, but had no effect on [Ca2+]i transient amplitude. 4. Our data are consistent with increased myofilament Ca2+ sensitivity when there is reduced binding of C-protein to myosin near the head-tail junction. 5. We propose that the effects of introducing S2 into intact cardiac cells can be equated with the consequences of selectively phosphorylating C-protein in vivo, and that the regulation of contraction by C-protein is mediated by the effects of crossbridge cycling on the Ca2+ affinity of troponin C.

Cryo-atomic force microscopy of smooth muscle myosin

The motor and regulatory domains of the head and the 14-nm pitch of the alpha-helical coiled-coil of the tail of extended (6S) smooth-muscle myosin molecules were imaged with cryo atomic force microscopy at 80-85 K, and the effects of thiophosphorylation of the regulatory light chain were examined. The tail was 4 nm shorter in thiophosphorylated than in nonphosphorylated myosin. The first major bend was invariant, at approximately 51 nm from the head-tail junction (H-T), coincident with low probability in the paircoil score. The second major bend was 100 nm from the H-T junction in nonphosphorylated and closer to a skip residue than the bend (at 95 nm) in thiophosphorylated molecules. The shorter tail and distance between the two major bends induced by thiophosphorylation are interpreted to result from melting of the coiled-coil. An additional bend not previously reported occurred, with a lower frequency, approximately 24 nm from the H-T. The range of separation between the two heads was greater in thiophosphorylated molecules. Occasional high-resolution images showed slight unwinding of the coiled-coil of the base of the heads. We suggest that phosphorylation of MLC20 can affect the structure of extended, 6S myosin.

Dynamic behaviour of the head-tail junction of myosin

It has generally been supposed that flexibility in the head-tail junction of myosin is provided by free rotation around the bonds of the polypeptide backbone of a few amino acid residues, but direct evidence for this is lacking. Here it is shown that the binding of an antibody in this region reveals a novel structure in which the bases of the heads are separated by 10 nm, with concomitant 9 nm shortening of the tail and movement of the sites of sharp bends in the tail a similar distance towards the heads. These results suggest that the junction is a dynamic structure in which between 60 and 130 residues of the coiled coil can separate to allow the heads to move apart. They suggest a site for the series elastic element of the cross-bridge, and have implications for the interactions of the two heads with actin subunits in the thin filaments, and the mechanism of movement of other two-headed motor proteins, such as kinesins.

Coiled-coil packing in spermine-induced tropomyosin crystals. A comparative study of three forms

Electron microscope images of highly ordered spermine-induced microcrystals of tropomyosin have been analyzed to determine the packing of the molecular filaments. Negatively stained microcrystals terminate in a distinctive "double fringe", which reveals the location of the molecular ends. This information, together with the symmetry of the structure in projection, shows that the microcrystals can be accounted for by a packing scheme of four layers of molecules in the unit cell. Knowing the position of the symmetry elements relating the layers then allows the three-dimensional space group of the microcrystals to be established as C222(1). Using cryo-electron microscopy and simulation studies, the run of the filaments and their packing in the C222(1) form have been shown to be related to those in the spermine-induced C2 crystal of tropomyosin whose structure has been solved to 9 A by X-ray crystallography. This result allows us to infer the location of the molecular ends in the C2 crystal as well, and this inference has been confirmed by analysis of thin sections of the C2 crystal. The C222(1) microcrystal has also been shown to be closely related to the classical divalent cation tropomyosin paracrystal. Based on knowledge of the molecular packing in the divalent cation paracrystal, the polarity of the molecules has been deduced in the other two crystal forms. The tropomyosin filament packing in all these forms may be accounted for by coiled-coil close packing and specific cationic bridging of negatively charged zones on the molecule. Taken together the results reveal a hierarchy of interactions in these close-packed crystalline forms, whose principles may apply to the packing in other fibrous proteins. This study also shows the usefulness of co-ordinating results from cryo-electron microscopy with negative staining in the structure analysis of such ordered arrays, and how these findings can complement the results of low resolution X-ray crystallographic studies.

Pitch diversity in alpha-helical coiled coils

Two complementary methods for measuring local pitch based on heptad position in alpha-helical coiled coils are described and applied to six crystal structures. The results reveal a diversity of pitch values: two-stranded coiled coils appear to have pitch values near 150 A; the values for three- and four-stranded coiled coils range closer to 200 A. The methods also provide a rapid and sensitive gauge of local coiled-coil conformation. Polar or charged residues in the apolar interface between coiled-coil helices markedly affect local pitch values, suggesting a connection between pitch uniformity and coiled-coil stability. Moreover, the identification of a skip residue (heptad frame shift) in the hemagglutinin glycoprotein of influenza virus (HA) allows interpretation of local pitch changes. These results on relatively short coiled-coil structures have relevance for the much longer fibrous proteins (many of which have skip residues) whose detailed structures are not yet established. We also show that local pitch values from molecular dynamics predictions of the GCN4 leucine zipper are in striking agreement with the high-resolution crystal structure--a result not readily discerned by direct comparison of atomic coordinates. Taken together, these methods reveal specific aspects of coiled-coil structure which may escape detection by global analyses of pitch.

Structure of tropomyosin at 9 angstroms resolution

We have used molecular replacement followed by a highly parameterized refinement to determine the structure of tropomyosin crystals to a resolution to 9 A. The shape, coiled-coil structure and interactions of the molecules in the crystals have been determined. These crystals have C2 symmetry with a = 259.7 A, b = 55.3 A, c = 135.6 A and beta = 97.2 degrees. Because of the unusual distribution of intensity in X-ray diffraction patterns from these crystals, it was possible to solve the rotation problem by inspection of qualitative aspects of the diffraction data and to define unequivocally the general alignment of the molecules along the (332) and (3-32) directions of the unit cell. The translation function was then solved by a direct search procedure, while electron microscopy of a related crystal form indicated the probable location of molecular ends in the asymmetric unit, as well as the anti-parallel arrangement. The structural model we have obtained is much clearer than that obtained previously with crystals of extraordinarily high solvent content and shows the two alpha-helices of the coiled coil over most of the length of the molecules and establishes the coiled-coil pitch at 140(+/- 10) A. Moreover, the precise value of the coiled-coil pitch varies along the molecule, probably in response to local variations in the amino acid sequence, which we have determined by sequencing the appropriate cDNA. The crystals are constructed from layers of tropomyosin filaments. There are two molecules in the crystallographic asymmetric unit and the molecules within a layer are bent into an approximately sinusoidal profile. Molecules in consecutive layers in the crystal lie at an angle relative to one another as found in crystalline arrays of actin and myosin rod. There are three classes of interactions between tropomyosin molecules in the spermine-induced crystals and these give some insights into the molecular interactions between coiled-coil molecules that may have implications for assemblies such as muscle thick filaments and intermediate filaments. In interactions within a layer, the geometry of coiled-coil contacts is retained, whereas in contacts between molecules in adjacent layers the coiled-coil geometry varies and these interactions instead appear to be dominated by the repeating pattern of charged zones along the molecule.

Role of the COOH-terminal nonhelical tailpiece in the assembly of a vertebrate nonmuscle myosin rod

A short nonhelical sequence at the COOH-terminus of vertebrate nonmuscle myosin has been shown to enhance myosin filament assembly. We have analyzed the role of this sequence in chicken intestinal epithelial brush border myosin, using protein engineering/site-directed mutagenesis. Clones encoding the rod region of this myosin were isolated and sequenced. They were truncated at various restriction sites and expressed in Escherichia coli, yielding a series of mutant myosin rods with or without the COOH-terminal tailpiece and with serial deletions from their NH2-termini. Deletion of the 35 residue COOH-terminal nonhelical tailpiece was sufficient to increase the critical concentration for myosin rod assembly by 50-fold (at 150 mM NaCl, pH 7.5), whereas NH2-terminal deletions had only minor effects. The only exception was the longest NH2-terminal deletion, which reduced the rod to 119 amino acids and rendered it assembly incompetent. The COOH-terminal tailpiece could be reduced by 15 amino acids and it still efficiently promoted assembly. We also found that the tailpiece promoted assembly of both filaments and segments; assemblies which have different molecular overlaps. Rod fragments carrying the COOH-terminal tailpiece did not promote the assembly of COOH-terminally deleted material when the two were mixed together. The tailpiece sequence thus has profound effects on assembly, yet it is apparently unstructured and can be bisected without affecting its function. Taken together these observations suggest that the nonhelical tailpiece may act sterically to block an otherwise dominant but unproductive molecular interaction in the self assembly process and does not, as has been previously thought, bind to a specific target site(s) on a neighboring molecule.

Tris-tricine and Tris-borate buffer systems provide better estimates of human mesothelial cell intermediate filament protein molecular weights than the standard Tris-glycine system

Human mesothelial cells contain a number of well defined intermediate filament proteins (IFs) that have been completely sequenced including vimentin and the cytokeratins (K7, K8, K18, and K19). The electrophoretic migration of these IFs was monitored as a function of second dimension gel buffer composition using various systems including Tris-glycine (pH 8.3 or 9.2), Tris-glycine with 20% methanol, Tris-borate, Tris-tricine, and sodium phosphate. All of the second dimension buffer chemistries yielded patterns of sufficient resolution to identify the major cytoskeletal proteins but differed in the relative mobilities of the IFs. Using gene sequence calculated molecular weight data, the major cytoskeletal polypeptides of human mesothelial cells were ranked from highest molecular weight to lowest molecular weight. This rank order of sequence calculated molecular weights was then compared to the rank order determined form the actual migration of the polypeptides in the different gel systems. With the Tris-tricine and the Tris-borate gel systems as well as gene sequence data, KS = vimentin greater than beta-tubulin = K7 greater than K18 greater than K19 greater than actin. With the pH 8.3 and 9.2 Tris-glycine systems, as well as the sodium phosphate gel system, the rank order of the polypeptides did not correspond to gene sequence data. Adding 20% methanol to the Tris-glycine system resulted in IF migration that more closely corresponded to the gene sequence derived data. Migration position of the IFs depended upon the temperature of the second dimension separation as well. In mesothelial cells, the migration of a total of 15-25% of the polypeptides was influenced by differing buffer systems.(ABSTRACT TRUNCATED AT 250 WORDS)

Three-dimensional structure of frozen-hydrated paracrystals of myosin rod

Myosin rod, the tail fragment of myosin, aggregates into various structures at physiological ionic strength. One form, the type II paracrystal, a thin, ribbon-like species, has recently been studied using conventional electron microscopy and was shown to possess two-dimensional order and, further, is likely to be useful in the investigation of the arrangement of myosin molecules in the backbone of the vertebrate muscle thick filament (Ward & Bennett, 1989). We have now examined this aggregate in the frozen-hydrated state by cryo-electron microscopy. Image analysis indicated that the projected structure has the same p12, plane group symmetry as seen after negative staining. A three-dimensional map, calculated from projections, indicated that the structure comprises a bilayer arrangement of strands of grouped rod molecules, with the strands parallel in each layer. The layers themselves are related by screw symmetry. Strands in adjacent layers have opposing polarity with their long axes at an angle of 32 degree to each other. Protein density measurements, carried out on unstained specimens using electron energy-loss spectroscopy, showed that the 44 X 13 X 13 nm unit cell is composed of 40% protein. The density measurements indicated that 9-12 rod molecules pass through each strand. Modelling rod molecules with 43 nm parallel overlaps in a body-centered tetragonal lattice produced a strand that compared favorably with the reconstructed strand. The size and content of these strands suggests that they are analogous to subfilaments observed in the vertebrate myosin thick filament.

High-resolution spot-scan electron microscopy of microcrystals of an alpha-helical coiled-coil protein

We describe the electron microscopy of a crystalline assembly of an alpha-helical coiled-coil protein extracted from the ootheca of the praying mantis. Electron diffraction patterns of unstained crystals show crystal lattice sampling of the coiled-coil molecular transform to a resolution beyond 1.5 A. Using a "spot-scan" method of electron imaging, micrographs of unstained crystals have been obtained that visibly diffract laser light from crystal spacings as small as 4.3 A. A projection map was calculated to 4 A using electron diffraction amplitudes and phases from computer-processed images. The projection map clearly shows modulations in density arising from the 5.1 A alpha-helical repeat, the first time this type of modulation has been revealed by electron microscopy. The crystals have p2 plane group symmetry with a = 92.4 A, b = 150.7 A, y = 92.4 degrees. Examination of tilted specimens shows that c is approximately 18 A, indicating that the unit cell is only one molecule thick. A preliminary interpretation shows tightly packed molecules some 400 A long lying with their long axes in the plane of the projection. The molecules have a coiled-coil configuration for most of their length. The possible modes of packing of the molecules in three dimensions are discussed.

Elucidating the early stages of keratin filament assembly

Because of extraordinarily tight coiled-coil associations of type I and type II keratins, the composition and structure of keratin subunits has been difficult to determine. We report here the use of novel genetic and biochemical methods to explore the early stages of keratin filament assembly. Using bacterially expressed humans K5 and K14, we show that remarkably, these keratins behave as 1:1 complexes even in 9 M urea and in the presence of a reducing agent. Gel filtration chromatography and chemical cross-linking were used to identify heterodimers and heterotetramers as the most stable building blocks of keratin filament assembly. EM suggested that the dimer consists of a coiled-coil of K5 and K14 aligned in register and in parallel fashion, and the tetramer consists of two dimers in antiparallel fashion, without polarity. In 4 M urea, both end-to-end and lateral packing of tetramers occurred, leading to a variety of larger heteromeric complexes. The coexistence of multiple, higher-ordered associations under strongly denaturing conditions suggests that there may not be a serial sequence of events leading to the assembly of keratin intermediate filaments, but rather a number of associations may take place in parallel.

Expression of Dictyostelium myosin tail segments in Escherichia coli: domains required for assembly and phosphorylation

The assembly of myosins into filaments is a property common to all conventional myosins. The ability of myosins to form filaments is conferred by the tail of the large asymmetric molecule. We are studying cloned portions of the Dictyostelium myosin gene expressed in Escherichia coli to investigate functional properties of defined segments of the myosin tail. We have focused on five segments derived from the 68-kD carboxyl-terminus of the myosin tail. These have been expressed and purified to homogeneity from E. coli, and thus the boundaries of each segment within the myosin gene and protein sequence are known. We identified an internal 34-kD segment of the tail, N-LMM-34, which is required and sufficient for assembly. This 287-amino acid domain represents the smallest tail segment purified from any myosin that is capable of forming highly ordered paracrystals characteristic of myosin. Because the assembly of Dictyostelium myosin can be regulated by phosphorylation of the heavy chain, we have studied the in vitro phosphorylation of the expressed tail segments. We have determined which segments are phosphorylated to a high level by a Dictyostelium myosin heavy chain kinase purified from developed cells. While LMM-68, the 68-kD carboxyl terminus of Dictyostelium myosin, or LMM-58, which lacks the 10-kD carboxyl terminus of LMM-68, are phosphorylated to the same extent as purified myosin, subdomains of these segments do not serve as efficient substrates for the kinase. Thus LMM-58 is one minimal substrate for efficient phosphorylation by the myosin heavy chain kinase purified from developed cells. Taken together these results identify two functional domains in Dictyostelium myosin: a 34-kD assembly domain bounded by amino acids 1533-1819 within the myosin sequence and a larger 58-kD phosphorylation domain bounded by amino acids 1533-2034 within the myosin sequence.

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.

Sequence analysis of the complete Caenorhabditis elegans myosin heavy chain gene family

The sequences of three myosin heavy chain (MHC) genes from Caenorhabditis elegans, myo-1, 2 and 3, are presented. These genes, together with unc-54, comprise the entire nematode sacromeric MHC family. Comparison of nematode MHC sequences and sarcomeric, smooth and non-muscle MHCs from other organisms highlights conserved sequence features of the MHC rod believed to be important for thick filament assembly. These include: conservation of sequence differences between individual 28 amino acid repeats; invariant placements of large aromatic residues, such as tryptophan, in the rod sequences; conservation of "weak spots" in the hydrophobic seam; and conservation of non-uniform charge distributions along the length of the rod. The rod sequences of the body wall isoforms A and B are more closely related to each other than to the pharyngeal isoforms C and D, suggesting that structural constraints have been imposed by their location within the same thick filament. We have also identified the major transcriptional start site for gene unc-54. Surprisingly, there are no TATA or other known transcription factor elements immediately upstream from the unc-54 start site, or in the upstream regions of the other genes of the C. elegans MHC gene family.

Paracrystals of myosin rod

To help understand the packing of myosin tails in the backbone of the vertebrate striated muscle thick filament, paracrystals of myosin rod, a proteolytic fragment corresponding to the whole myosin tail, have been examined by electron microscopy and image analysis. Two types of paracrystal were observed. Type I paracrystals were similar to those seen by Moos et al. (1975; J. molec. Biol. 97, 1-9). These showed a 14-nm axial repeat, but yielded no other structural information. Type II paracrystals were long, flexible ribbons with more regularity. When negatively stained they exhibited a weak 43-nm axial striation and appeared to be composed of a layer of narrow filaments. Optical diffraction showed that the paracrystals had a rectangular unit cell of dimensions 43 nm axially and 12.4 nm laterally. Transverse sections indicated a paracrystal depth similar to the lateral dimension of the unit cell. Each unit cell contained two filaments arranged antiparallel and related by a two-fold screw axis perpendicular to the length, and in the plane of the ribbon. The filaments probably consist of parallel rod molecules related by axial displacements of 43 nm and higher multiples of 43 nm. The nature of these paracrystals indicates that the myosin tail alone can form structures like thick filament subfilaments. Their structure, based on distinguishable parallel and antiparallel rod interactions, was sensitive to pH and divalent cations in a similar way to the ionic effects on the structure of thick filaments. This behaviour suggests that some of the interactions present in the paracrystal are the same as those in the thick filament.

Segmented alpha-helical coiled-coil structure of the protein giardin from the Giardia cytoskeleton

The parasitic flagellate Giardia is the source of a filamentous protein, giardin, which binds to microtubules. The primary sequence of one giardin chain has been decoded from the base sequences of cDNAs isolated by antibody screens of a library constructed in the expression vector lambda gt11. The amino acid sequence favours a continuous alpha-helical fold for the protein without any inserts of a non-helical character. Analysis of apolar residue positions revealed 35 repeating heptads consistent with coiled-coil structure. This conformation relates giardin to the alpha-type fibrous proteins (k-m-e-f class) like tropomyosin and myosin (also found in Giardia). The giardin sequence has a regular series of skip residues like those at certain positions in the rod section of nematode myosin where the internal apolar seam of the coiled coil is shifted on the helix surface. The skips divide the giardin coil into quasi-equivalent structural segments about 4 nm in length, which might be domains for combining with tubulin subunits in the microtubule surface lattice.

An X-ray diffraction study of alpha-tropomyosin magnesium tactoid

The structure of the needle-shaped aggregate of alpha-tropomyosin formed in the presence of Mg2+ ions (the Mg-tactoid) was studied by X-ray diffraction. Orientated specimens were prepared by magnetic orientation. The meridional reflections corresponding to a Bragg spacing of up to 2.6 nm were recorded and phased by the isomorphous replacement method using p-chloromercuribenzoate bound to the unique cysteine residue of the alpha-chain of tropomyosin. The axial electron density profile thus obtained was compared with the model proposed from electron microscopic investigations. With an adequate phase combination for the observed intensities, the agreement was satisfactory. Comparison with electron micrographs of negatively stained Mg-tactoids suggests that the C-terminus of the molecule has an extended conformation and penetrates into the N-N overlap region. The principal repeat length along the tactoid was 39.0 nm, which was about 5% shorter than the expected periodicity of the tropomyosin molecules with an end-to-end overlap of eight residues, suggesting supercoiling. The equatorial reflections consisted of the diffuse peaks at 1/8 nm-1 and 1/2.3 nm-1. The former indicates, for the first time, the presence of a large structural unit with low crystallinity. The spacing of the latter probably corresponds to the average centre-to-centre distance between neighbouring tropomyosin molecules.

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.