Distinct roles of 1alpha and 1beta heavy chains of the inner arm dynein I1 of Chlamydomonas flagella

The Chlamydomonas I1 dynein is a two-headed inner dynein arm important for the regulation of flagellar bending. Here we took advantage of mutant strains lacking either the 1α or 1β motor domain to distinguish the functional role of each motor domain. Single- particle electronic microscopic analysis confirmed that both the I1α and I1β complexes are single headed with similar ringlike, motor domain structures. Despite similarity in structure, however, the I1β complex has severalfold higher ATPase activity and microtubule gliding motility compared to the I1α complex. Moreover, in vivo measurement of microtubule sliding in axonemes revealed that the loss of the 1β motor results in a more severe impairment in motility and failure in regulation of microtubule sliding by the I1 dynein phosphoregulatory mechanism. The data indicate that each I1 motor domain is distinct in function: The I1β motor domain is an effective motor required for wild-type microtubule sliding, whereas the I1α motor domain may be responsible for local restraint of microtubule sliding.     

X-ray diffraction recording from single axonemes of eukaryotic flagella

We report the first X-ray diffraction patterns recorded from single axonemes of eukaryotic flagella with a diameter of only <0.2 μm, by using the technique of cryomicrodiffraction. A spermatozoon isolated from the testis of a fruit fly, Drosophila melanogaster, either intact or demembranated, was mounted straight in a glass capillary, quickly frozen and its 800-μm segment was irradiated end-on with intense synchrotron radiation X-ray microbeams (diameter, ~2 μm) at 74 K. Well-defined diffraction patterns were recorded, consisting of a large number of isolated reflection spots, extending up to 1/5 nm(-1). These reflections showed a tendency to peak every 20°, i.e., the patterns had features of an 18-fold rotational symmetry as expected from the 9-fold rotational symmetry of axonemal structure. This means that the axonemes remain untwisted, even after the manual mounting procedure. The diffraction patterns were compared with the results of model calculations based on a published electron micrograph of the Drosophila axoneme. The comparison provided information about the native state of axoneme, including estimates of axonemal diameter, interdoublet spacing, and masses of axonemal components relative to those of microtubules (e.g., radial spokes, dynein arms, and proteins associated with accessory singlet microtubules). When combined with the genetic resource of Drosophila, the technique presented here will serve as a powerful tool for studying the structure-function relationship of eukaryotic flagella in general.     

Control of actin moving trajectory by patterned poly(methylmethacrylate) tracks.

Poly(methylmethacrylate) (PMMA), a photoresist polymer, was found to be useful for immobilizing heavy meromyosin (HMM) molecules while retaining their abilities to support the movement of actin filaments. PMMA substrate was spin-coated on a coverslip, and various shapes of PMMA tracks, such as straight lines, concentric circles, and alphabetical letters, were fabricated by UV photolithography. An observation by a Tapping mode atomic force microscope (AFM) shows that the typical circular tracks were 1-2 microns wide and about 200 nm high. In in vitro motility assay, a solution of HMM molecules was applied to immobilize the molecules on the tracks by adsorption, and movement of actin filaments labeled with tetramethylrhodamine-phalloidin were observed in the presence of ATP by using an epifluorescence microscope and an image-intensified CCD camera. Actin filaments were seen to move precisely only on the PMMA tracks, and their traces drew the exact shapes of the tracks. The mean velocity of actin movement on the PMMA was 4.5 mm/s at 25 degrees C, and it was comparable to that on a conventionally used nitrocellulose film.     

Controlling the direction of kinesin-driven microtubule movements along microlithographic tracks

Motor proteins are able to move protein filaments in vitro. However, useful work cannot be extracted from the existing in vitro systems because filament motions are in random directions on two-dimensional surfaces. We succeeded in restricting kinesin-driven movements of microtubules along linear tracks by using micrometer-scaled grooves lithographically fabricated on glass surfaces. We also accomplished the extraction of unidirectional movement from the bidirectional movements along the linear tracks by adding arrowhead patterns on the tracks. These "rectifiers" enabled us to construct microminiturized circulators in which populations of microtubules rotated in one direction, and to actively transport microtubules between two pools connected by arrowheaded tracks in the fields of micrometer scales.     

X-ray diffraction evidence for the lack of stereospecific protein interactions in highly activated actomyosin complex

The structure of actomyosin complex while hydrolyzing ATP was investigated by recording X-ray diffraction patterns from rabbit skeletal muscle fibers, in which exogenously introduced rabbit skeletal subfragment-1 (S1) was covalently cross-linked to the endogenous actin filaments in rigor by 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC). Approximately two-thirds of the introduced S1 was cross-linked. The cross-linking procedure did not affect the profile of the S1-induced enhancement of the actin-based layer line reflections in rigor, indicating that the acto-S1 interactions remained highly stereospecific. In the presence of ATP, the MgATPase of the S1 was highly activated regardless of calcium levels, presumably because the availability of the stereospecific binding sites for both proteins was maximized by the cross-linking. However, the diffraction pattern in the presence of ATP was striking in that the intensity profile of the strong 1/5.9 nm(-1) layer lines was indistinguishable from that from bare actin filaments, despite the fact that the majority of the S1 was still associated with actin. The change of the intensity profiles upon addition of ATP was completely reversible. Model calculations showed that this result can be explained if the S1 is not only swinging around its pivoting point, but the pivoting point itself is also moving on the actin surface in a range of a few nanometers. The results suggest that the stereospecific binding sites, which have been considered important for actomyosin cycling, are paradoxically left unoccupied for most of the time in this highly activated actomyosin complex.     

The structure of dynein-c by negative stain electron microscopy

Dynein ATPases contain six concatenated AAA modules within the motor region of their heavy chains. Additional regions of sequence are required to form a functional ATPase, which a previous study suggested forms seven or eight subdomains arranged in either a ring or hollow sphere. A more recent homology model of the six AAA modules suggests that these form a ring. Therefore both the number and arrangement of subdomains remain uncertain. We show two-dimensional projection images of dynein-c in negative stain which reveal new details of its structure. Initial electron cryomicroscopy shows a similar overall morphology. The molecule consists of three domains: stem, head, and stalk. In the absence of nucleotide the head has seven lobes of density forming an asymmetric ring. An eighth lobe protrudes from one side of this heptameric ring and appears to join the elongated cargo-binding stem. The proximal stem is flexible, as is the stalk, suggesting that they act as compliant elements within the motor. A new analysis of pre- and post-power stroke conformations shows the combined effect of their flexibility on the spatial distribution of the microtubule-binding domain and therefore the potential range of power stroke sizes. We present and compare two alternative models of the structure of dynein.     

Self-similar mitochondrial DNA

We show that repeated sequences, like palindromes (local repetitions) and homologies between two different nucleotide sequences (motifs along the genome), compose a self-similar (fractal) pattern in mitochondrial DNA. This self-similarity comes from the looplike structures distributed along the genome. The looplike structures generate scaling laws in a pseudorandom DNA walk constructed from the sequence, called a Lévy flight. We measure the scaling laws from the generalized fractal dimension and singularity spectrum for mitochondrial DNA walks for 35 different species. In particular, we report characteristic loop distributions for mammal mitochondrial genomes.     

Catchin, a novel protein in molluscan catch muscles, is produced by alternative splicing from the myosin heavy chain gene

Molluscan catch muscles contain polypeptides of 110-120 kDa in size which have the same partial amino acid sequences as those of the myosin heavy chain (MHC). Here we provide evidence that these polypeptides are major components only of the catch-type muscles (their estimated molar ratio to MHC is approximately 1:1) and they are alternative products of the MHC gene. Northern blot analysis of total RNA from Mytilus galloprovincialis catch muscles was carried out with fragments from the 3'-end of the MHC cDNA as probes. We detected two bands of 6.5 kb and 3.5 kb. The former corresponds to the MHC mRNA, and the latter is an mRNA coding for catchin, a novel myosin rod-like protein. By using a 5'-rapid amplification of cDNA ends (RACE) PCR method, the full-length cDNA of Mytilus catchin was cloned. It codes for a protein with a unique N-terminal domain of 156 residues (rich in serine, threonine, and proline), which includes a phosphorylatable peptide sequence. The rest of the sequence is identical with the C-terminal 830 residues of the MHC. We also analyzed Mytilus and scallop (Argopecten irradians) genomic DNAs and found that the 5'-end of the cDNA sequence was located in a large intron of the MHC gene in both species. Since catchin is abundantly expressed only in catch muscles and it is phosphorylatable, we suggest that it may play an important role in the catch contraction of molluscan smooth muscles.     

The architecture of outer dynein arms in situ

Outer dynein arms, the force generators for axonemal motion, form arrays on microtubule doublets in situ, although they are bouquet-like complexes with separated heads of multiple heavy chains when isolated in vitro. To understand how the three heavy chains are folded in the array, we reconstructed the detailed 3D structure of outer dynein arms of Chlamydomonas flagella in situ by electron cryo-tomography and single-particle averaging. The outer dynein arm binds to the A-microtubule through three interfaces on two adjacent protofilaments, two of which probably represent the docking complex. The three AAA rings of heavy chains, seen as stacked plates, are connected in a striking manner on microtubule doublets. The tail of the alpha-heavy chain, identified by analyzing the oda11 mutant, which lacks alpha-heavy chain, extends from the AAA ring tilted toward the tip of the axoneme and towards the inside of the axoneme at 50 degrees , suggesting a three-dimensional power stroke. The neighboring outer dynein arms are connected through two filamentous structures: one at the exterior of the axoneme and the other through the alpha-tail. Although the beta-tail seems to merge with the alpha-tail at the internal side of the axoneme, the gamma-tail is likely to extend at the exterior of the axoneme and join the AAA ring. This suggests that the fold and function of gamma-heavy chain are different from those of alpha and beta-chains.     

Coupling of rotation and catalysis in F(1)-ATPase revealed by single-molecule imaging and manipulation

F(1)-ATPase is a rotary molecular motor that proceeds in 120 degrees steps, each driven by ATP hydrolysis. How the chemical reactions that occur in three catalytic sites are coupled to mechanical rotation is the central question. Here, we show by high-speed imaging of rotation in single molecules of F(1) that phosphate release drives the last 40 degrees of the 120 degrees step, and that the 40 degrees rotation accompanies reduction of the affinity for phosphate. We also show, by single-molecule imaging of a fluorescent ATP analog Cy3-ATP while F(1) is forced to rotate slowly, that release of Cy3-ADP occurs at approximately 240 degrees after it is bound as Cy3-ATP at 0 degrees . This and other results suggest that the affinity for ADP also decreases with rotation, and thus ADP release contributes part of energy for rotation. Together with previous results, the coupling scheme is now basically complete.