Skip Residues Research Articles

SF-assemblin, the structural protein of the 2-nm filaments from striated microtubule associated fibers of algal flagellar roots, forms a segmented coiled coil.

The microtubule associated system I fibers of the basal apparatus of the flagellate green alga Spermatozopsis similis are noncontractile and display a 28-nm periodicity. Paracrystals with similar periodicities are formed in vitro by SF-assemblin, which is the major protein component of system I fibers. We have determined the amino acid sequence of SF-assemblin and show that it contains two structural domains. The NH2-terminal 31 residues form a nonhelical domain rich in proline. The rod domain of 253 residues is alpha-helical and seems to form a segmented coiled coil with a 29-residue repeat pattern based on four heptads followed by a skip residue. The distinct cluster of acidic residues at the COOH-terminal end of the motifs (periodicity about 4 nm) may be related to tubulin binding of SF-assemblin and/or its self assembly. A similar structure has been predicted from cDNA cloning of beta-giardin, a protein of the complex microtubular apparatus of the sucking disc in the protozoan flagellate Giardia lamblia. Although the rod domains of SF-assemblin and beta-giardin share only 20% sequence identity, they have exactly the same length and display 42% sequence similarity. These results predict that system I fibers and related microtubule associated structures arise from molecules able to form a special segmented coiled coil which can pack into 2-nm filaments. Such molecules seem subject to a strong evolutionary drift in sequence but not in sequence principles and length. This conservation of molecular architecture may have important implications for microtubule binding.

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.

Cloning of the cDNA encoding a neuronal myosin heavy chain from mammalian brain and its differential expression within the central nervous system

The complete amino acid sequence of a neuronal myosin heavy chain (MHC) from mammalian brain (1999 amino acids, 230 kDa) has been deduced by sequencing cDNA clones isolated from a rat brain cDNA library. The library was screened using an affinity-purified polyclonal antibody that had been raised against myosin purified from a neuronally-derived cell line (Neuro-2A). Restriction digests of genomic DNA from Neuro-2A cells and rat brain are consistent with an identity of the sequenced isoform from these two sources. RNA blot analysis demonstrates this myosin to exhibit differential expression within the cerebral cortex and spinal cord. No expression was observed in liver, kidney, heart, spleen or skeletal muscle, or even within other regions of the brain. The sequence of this neuronal MHC is compared with those of other non-muscle MHCs, to which it shows an overall similarity of structure, especially with respect to conserved regions within the head (ATP binding site, actin binding site, reactive thiols) and the presence of an α-helical coiled-coil tail that can be arranged as 28-residue repeating units plus four skip residues. A unique non-helical tailpiece composed of 72 amino acid residues marks the C-terminus of this neuronal myosin isoform.

Proteolytic susceptibility of the central domain in chicken gizzard and skeletal muscle dystrophins

We investigated proteolytic susceptibility of the central domain in dystrophin molecules from chicken smooth and skeletal muscles. Dystrophin-enriched preparations from both muscles were made as described in Pons et al. (Proc. Natl. Acad. Sci. USA (1990) 87, 7851–7855). These preparations contained other protein components in addition to dystrophin. Three enzymes ( Staphyloccocus aureus proteinase, chymotrypsin and trypsin) having different proteolytic specificities were used. Time-courses fo proteinase degradation were examined by the Western immunoblot technique using a specific polyclonal serum directed against a fragment (residues 1173–1728) of the dystrophin central domain. We observed accumulation of some major proteinase-resistant fragments, in the 110–160 kDa range originating from that central region of the molecule. Cleavage patternsr of the smooth and skeletal muscle preparations were quite similar, but molecular weights of the breakdown products different slightly. Interpretation of the results was based on two predictive structural models of the dystrophin central domain (Koenig and Kunkel (1990) J. Biol. Chem. 265, 4560–4566 and Cross et al. (1990) FEBS lett. 262, 87–90). Skip residues at the end of repeat 13 (around the 1740th residue of the dystrophin amino acid sequence), as hypothesized in the Cross model, constitute probably the most sensitive site within the dystrophin central domain for any exogenous (of even endogenous) proteinase. Variations observed between dystrophins from skeletal and smooth muscles also suggest that the structures of both dystrophins differ slightly even within the dystrophin central domain. This precise identification of proteinase-resistant dystrophin fragments of variable lengths is a first setp towards further physiochemical studies on the very large and rare dystrophin molecule.

Expression in Escherichia coli of fragments of the coiled-coil rod domain of rabbit myosin: influence of different regions of the molecule on aggregation and paracrystal formation

We have expressed in Escherichia coli a cDNA clone corresponding broadly to rabbit light meromyosin (LMM) together with a number of modified polypeptides and have used this material to investigate the role of different aspects of molecular structure on the solubility properties of LMM. The expressed material was characterized biochemically and structurally to ensure that it retained the coiled-coil conformation of the native molecule. Full-length recombinant LMM retained the general solubility properties of myosin and, although soluble at high ionic strength, precipitated when the ionic strength was reduced below 0.3 M. Constructs in which the 'skip' residues (that disrupt the coiled-coil heptad repeat) were deleted had solubility properties indistinguishable from the wild type, which indicated that the skip residues did not play a major role in determining the molecular interactions involved in assembly. Deletions from the N terminus of LMM did not alter the solubility properties of the expressed material, but deletion of 92 residues from the C terminus caused a large increase in solubility at low ionic strength, indicating that a determinant important for interaction between LMM molecules was located in this region. The failure of deletions from the molecule's N terminus to alter its solubility radically suggested that the periodic variation of charge along the myosin rod may not be as important as proposed for determining the strength of binding between molecules and thus the solubility of myosin.

Skip residues correlate with bends in the myosin tail

Sharp bends have previously been observed in the tail of the skeletal myosin molecule at well-defined positions 44, 75 and 135 nm from the head-tail junction, and in vertebrate smooth myosin at two positions about 45 and 96 nm from this junction. The amino acid sequence of the heavy chain does not straightforwardly account for such bending on the original model of the tail in which an invariant proline residue is present at the head-tail junction and the repeating seven amino acid pattern of hydrophobic residues lies entirely in the tail. Recently, a revised model has been proposed by Rimm et al. in which the first seven to eight heptads lie in the heads. It is shown here that with this model the observed bends in the tail of skeletal myosin coincide with three of the four additional (skip) residues that interrupt the heptad repeat. It is concluded that the skip residues, by causing localized instability of the coiled-coil, are responsible for the bends. Smooth myosin lacks the second of these skip residues explaining the absence of a bend at 75 nm.

Segmented α-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 λgt11. The amino acid sequence favours a continuous α-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 α-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.

Periodic features in the amino acid sequence of nematode myosin rod

Properties of the amino acid sequence of the nematode myosin rod region, deduced from cloned DNA, are analysed. The rod sequence of 1117 residues contains a regular region of 1094 residues, which has features typical of an alpha-helical coiled coil, followed by a short non-helical tailpiece at the carboxyl end. The hydrophobic amino acids show the expected seven-residue pattern a, b, c, d, e, f, g, which is modulated by a longer repeat of 28-residue zones. In addition, there are four one-residue insertions, or skip residues, at the ends of zones, at positions 351, 548, 745 and 970. Myosin is considerably less hydrophobic than tropomyosin or alpha-keratin and the outer surface of the coiled coil is covered by clusters of positive and negatively charged amino acid side-chains. Molecular models suggest that the coiled coil is continuous throughout the rod, with an approximately uniform left-handed twist, except for a few turns of helix near each skip region, where the twist flattens out to accommodate the extra residue. Fourier transforms of the amino acid profiles show strong periodicities based on repeats of seven residues ( 7 2 and 7 3 ) and 28 residues (especially 28 3 and 28 9 ). The positive and negative charges each have strong 28 3 -residue periodicities that are out of phase with one another. The negative charges also show a 196 9 -residue modulation frequency, which may reflect the presence of a 196-residue structural unit in muscle, approximately 2 × 143 Å long. The distribution of charged amino acids suggests that electrostatic forces are dominant in forming the thick filament structure. Models that allow regular patterns of interacting charges are restricted and the simplest types are discussed.