Toshiro Oda

RIKEN, Вако, Saitama, Japan

Are you Toshiro Oda?

Claim your profile

Publications (19)131.08 Total impact

  • Tomoki Aihara, Toshiro Oda
    [Show abstract] [Hide abstract]
    ABSTRACT: Cofilin is an actin-binding protein that promotes F-actin depolymerization. It is well-known that cofilin-coated F-actin is more twisted than naked F-actin, and that the protomer is more tilted. However, the means by which the local changes induced by the binding of individual cofilin proteins proceed to the global conformational changes of the whole F-actin molecule remain unknown. Here we investigated the cofilin-induced changes in several parts of F-actin, through site-directed spin-label electron paramagnetic resonance spectroscopy analyses of recombinant actins containing single reactive cysteines. We found that the global, cooperative conformational changes induced by cofilin-binding, which were detected by the spin-label attached to the Cys374 residue, occurred without the detachment of the D-loop in subdomain 2 from the neighboring protomer. The two processes of local and global changes do not necessarily proceed in sequence.
    Biochemical and Biophysical Research Communications 05/2013; DOI:10.1016/j.bbrc.2013.04.076 · 2.28 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Actin plays fundamental roles in a variety of cell functions in eukaryotic cells. The polymerization - depolymerization cycle, between monomeric G-actin and fibrous F-actin, drives essential cell processes. Recently, we proposed the atomic model for the F-actin structure, and found that actin was in the twisted form in the monomer, and in the untwisted form in the filament. To understand how the polymerization process is regulated (Caspar (1991) Curr. Biol. 1, 30-32), we need to know further details about the transition from the twisted to the untwisted form. For this purpose, we focused our attention on the A108 - P112 loop, which must play crucial roles in the transition, and analyzed the consequences of the amino acid replacements on the polymerization process. As compared with the wild type, the polymerization of P109A was accelerated in both the nucleation and elongation steps, and this was attributed to an increase in the frequency factor of the Arrhenius equation. The multiple conformations allowed by the substitution presumably resulted in the effective formation of the collision complex, thus accelerating polymerization. On the other hand, the A108G mutation reduced the rates of both nucleation and elongation, due to an increase in the activation energy. In the cases of polymerization acceleration and deceleration, each functional aberration is attributed to a distinct elementary process. The rigidity of the loop, which mediates neither too strong nor too weak interactions between subdomains 1 and 3, might play crucial roles in actin polymerization.
    Journal of Biological Chemistry 11/2012; DOI:10.1074/jbc.M112.392019 · 4.60 Impact Factor
  • Biophysical Journal 01/2012; 102(3):372-. DOI:10.1016/j.bpj.2011.11.2034 · 3.83 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The actin filament has clear polarity where one end, the pointed end, has a much slower polymerization and depolymerization rate than the other end, the barbed end. This intrinsic difference of the ends significantly affects all actin dynamics in the cell, which has central roles in a wide spectrum of cellular functions. The detailed mechanism underlying this difference has remained elusive, because high-resolution structures of the filament ends have not been available. Here, we present the structure of the actin filament pointed end obtained using a single particle analysis of cryo-electron micrographs. We determined that the terminal pointed end subunit is tilted towards the penultimate subunit, allowing specific and extra loop-to-loop inter-strand contacts between the two end subunits, which is not possible in other parts of the filament. These specific contacts prevent the end subunit from dissociating. For elongation, the loop-to-loop contacts also inhibit the incorporation of another actin monomer at the pointed end. These observations are likely to account for the less dynamic pointed end.
    The EMBO Journal 03/2011; 30(7):1230-7. DOI:10.1038/emboj.2011.48 · 10.75 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: A large number of actin-binding proteins (ABPs) regulate various kinds of cellular events in which the superstructure of the actin cytoskeleton is dynamically changed. Thus, to understand the actin dynamics in the cell, the mechanisms of actin regulation by ABPs must be elucidated. Moreover, it is particularly important to identify the side, barbed-end or pointed-end ABP binding sites on the actin filament. However, a simple, reliable method to determine the ABP binding sites on the actin filament is missing. Here, a novel electron microscopic method for determining the ABP binding sites is presented. This approach uses a gold nanoparticle that recognizes a histidine tag on an ABP and an image analysis procedure that can determine the polarity of the actin filament. This method will facilitate future study of ABPs.
    Journal of Molecular Biology 02/2011; 408(1):26-39. DOI:10.1016/j.jmb.2011.01.054 · 3.96 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Spire is an actin nucleator that initiates actin polymerization at a specific place in the cell. Similar to the Arp2/3 complex, spire was initially considered to bind to the pointed end of the actin filament when it generates a new actin filament. Subsequently, spire was reported to be associated with the barbed end (B-end); thus, there is still no consensus regarding the end with which spire interacts. Here, we report direct evidence that spire binds to the B-end of the actin filament, under conditions where spire accelerates actin polymerization. Using electron microscopy, we visualized the location of spire bound to the filament by gold nanoparticle labeling of the histidine-tagged spire, and the polarity of the actin filament was determined by image analysis. In addition, our results suggest that multiple spires, linked through one gold nanoparticle, enhance the acceleration of actin polymerization. The B-end binding of spire provides the basis for understanding its functional mechanism in the cell.
    Journal of Molecular Biology 02/2011; 408(1):18-25. DOI:10.1016/j.jmb.2010.12.045 · 3.96 Impact Factor
  • Toshiro Oda, Yuichiro Maéda
    [Show abstract] [Hide abstract]
    ABSTRACT: Actin works within eukaryotic cells to facilitate a variety of cellular processes, which are driven by the assembly of G-actin (monomeric form) into F-actin (fibrous form), and the disassembly of F-actin into G-actin. F-actin adopts multiple conformations, which are specified by interactions with various actin-binding proteins. Knowledge of the multiple conformations of actin is the key for understanding its cellular functions. Recently, we published a refined model for F-actin. In this review, based on this model, we discuss the origin, mechanism, and possible physiological significance of the multiple conformations of F-actin.
    Structure 07/2010; 18(7):761-7. DOI:10.1016/j.str.2010.05.009 · 6.79 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: AlfA is a recently discovered DNA segregation protein from Bacillus subtilis that is distantly related to actin and the bacterial actin homologues ParM and MreB. Here we show that AlfA mostly forms helical 7/3 filaments, with a repeat of about 180 A, that are arranged in three-dimensional bundles. Other polymorphic structures in the form of two-dimensional rafts or paracrystalline nets were also observed. Here AlfA adopted a 16/7 helical symmetry, with a repeat of about 387 A. Thin polymers consisting of several intertwining filaments also formed. Observed helical symmetries of AlfA filaments differed from those of other members of the actin family: F-actin, ParM, or MreB. Both ATP and guanosine 5'-triphosphate are able to promote rapid AlfA filament formation with almost equal efficiencies. The helical structure is only preserved under physiological salt concentrations and at a pH between 6.4 and 7.4, the physiological range of the cytoplasm of B. subtilis. Polymerization kinetics are extremely rapid and compatible with a cooperative assembly mechanism requiring only two steps: monomer activation followed by elongation, making AlfA one of the most efficient polymerizing motors within the actin family. Phosphate release lags behind polymerization, and time-lapse total internal reflection fluorescence images of AlfA bundles are consistent with treadmilling rather than dynamic microtubule-like instability. High-pressure small angle X-ray scattering experiments reveal that the stability of AlfA filaments is intermediate between the stability of ParM and the stability of F-actin. These results emphasize that actin-like polymerizing machineries have diverged to produce a variety of filament geometries with diverse properties that are tailored for specific biological processes.
    Journal of Molecular Biology 02/2010; 397(4):1031-41. DOI:10.1016/j.jmb.2010.02.010 · 3.96 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: A hallmark of polyglutamine diseases, including Huntington disease (HD), is the formation of beta-sheet-rich aggregates, called amyloid, of causative proteins with expanded polyglutamines. However, it has remained unclear whether the polyglutamine amyloid is a direct cause or simply a secondary manifestation of the pathology. Here we show that huntingtin-exon1 (thtt) with expanded polyglutamines remarkably misfolds into distinct amyloid conformations under different temperatures, such as 4 degrees C and 37 degrees C. The 4 degrees C amyloid has loop/turn structures together with mostly beta-sheets, including exposed polyglutamines, whereas the 37 degrees C amyloid has more extended and buried beta-sheets. By developing a method to efficiently introduce amyloid into mammalian cells, we found that the formation of the 4 degrees C amyloid led to substantial toxicity, whereas the toxic effects of the 37 degrees C amyloid were very small. Importantly, thtt amyloids in different brain regions of HD mice also had distinct conformations. The thermolabile thtt amyloid with loop/turn structures in the striatum showed higher toxicity, whereas the rigid thtt amyloid with more extended beta-sheets in the hippocampus and cerebellum had only mild toxic effects. These studies show that the thtt protein with expanded polyglutamines can misfold into distinct amyloid conformations and, depending on the conformations, the amyloids can be either toxic or nontoxic. Thus, the amyloid conformation of thtt may be a critical determinant of cytotoxicity in HD.
    Proceedings of the National Academy of Sciences 07/2009; 106(24):9679-84. DOI:10.1073/pnas.0812083106 · 9.81 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: ParM, an actin homolog, forms left-handed two-start helical filaments that segregate DNA in bacteria prior to cell division. Our recent atomic model obtained from electron microscopy (EM) reconstructions of negatively stained ParM filaments implied that two salt bridges (Glu35-Lys258 and Asp63-Arg262) may be key inter-filament contacts that stabilize the left-handed ParM helix. We made mutations of these amino acids and probed the inter-strand interface of our model experimentally by EM and X-ray fiber diffraction. We found that several mutations, such as ParM single mutants Asp258 and Asp262 and double mutant Asp258/Arg262, were incapable of forming straight filaments in aqueous buffers and appeared ragged and unstructured. However, in the presence of crowding agents, straight filaments or filament bundles formed, which allowed us to elucidate the structure of these mutant filaments. Centrifugation of filaments also resulted in a pellet of straightened filaments that could be oriented in glass capillaries and gave detailed X-ray diffraction patterns. Both EM and X-ray diffraction showed that filaments formed from these ParM mutants were not double-stranded helical filaments but single protofilaments, indicating that these residues are important for formation of the ParM helix. Our data also confirm a major prediction of crowding theory, namely that molecular crowding shifts the equilibrium of even severely impaired, unstructured cytoskeletal polymers toward their structured native and functional state. ParM is the first example of a helical actin homolog that can be induced to form protofilaments.
    Journal of Molecular Biology 04/2009; 388(2):209-17. DOI:10.1016/j.jmb.2009.02.057 · 3.96 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Actin plays crucial parts in cell motility through a dynamic process driven by polymerization and depolymerization, that is, the globular (G) to fibrous (F) actin transition. Although our knowledge about the actin-based cellular functions and the molecules that regulate the G- to F-actin transition is growing, the structural aspects of the transition remain enigmatic. We created a model of F-actin using X-ray fibre diffraction intensities obtained from well oriented sols of rabbit skeletal muscle F-actin to 3.3 A in the radial direction and 5.6 A along the equator. Here we show that the G- to F-actin conformational transition is a simple relative rotation of the two major domains by about 20 degrees. As a result of the domain rotation, the actin molecule in the filament is flat. The flat form is essential for the formation of stable, helical F-actin. Our F-actin structure model provides the basis for understanding actin polymerization as well as its molecular interactions with actin-binding proteins.
    Nature 02/2009; 457(7228):441-5. DOI:10.1038/nature07685 · 42.35 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: The actin filament is quite dynamic in the cell. To determine the relationship between the structure and the dynamic properties of the actin filament, experiments using actin mutants are indispensable. We focused on Gln(137) to understand the relationships between two activities: the conformational changes relevant to the G- to F-actin transition and the activation of actin ATPase upon actin polymerization. To elucidate the function of Gln(137) in these activities, we characterized Gln(137) mutants of human cardiac muscle alpha-actin. Although all of the single mutants, Q137E, Q137K, Q137P, and Q137A, as well as the wild type were expressed by a baculovirus-based system, only Q137A and the wild type were purified to high homogeneity. The CD spectrum of Q137A was similar to that of the wild type, and Q137A showed the typical morphology of negatively stained Q137A F-actin images. However, Q137A had an extremely low critical concentration for polymerization. Furthermore, we found that Q137A polymerized 4-fold faster, cleaved the gamma-phosphate group of bound ATP 4-fold slower, and depolymerized 5-fold slower, as compared with the wild-type rates. These results suggest that Gln(137) plays dual roles in actin polymerization, in both the conformational transition of the actin molecule and the mechanism of ATP hydrolysis.
    Journal of Biological Chemistry 08/2008; 283(30):21045-53. DOI:10.1074/jbc.M800570200 · 4.60 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: ParM is a prokaryotic actin homologue, which ensures even plasmid segregation before bacterial cell division. In vivo, ParM forms a labile filament bundle that is reminiscent of the more complex spindle formed by microtubules partitioning chromosomes in eukaryotic cells. However, little is known about the underlying structural mechanism of DNA segregation by ParM filaments and the accompanying dynamic instability. Our biochemical, TIRF microscopy and high-pressure SAX observations indicate that polymerization and disintegration of ParM filaments is driven by GTP rather than ATP and that ParM acts as a GTP-driven molecular switch similar to a G protein. Image analysis of electron micrographs reveals that the ParM filament is a left-handed helix, opposed to the right-handed actin polymer. Nevertheless, the intersubunit contacts are similar to those of actin. Our atomic model of the ParM-GMPPNP filament, which also fits well to X-ray fibre diffraction patterns from oriented gels, can explain why after nucleotide release, large conformational changes of the protomer lead to a breakage of intra- and interstrand interactions, and thus to the observed disintegration of the ParM filament after DNA segregation.
    The EMBO Journal 03/2008; 27(3):570-9. DOI:10.1038/sj.emboj.7601978 · 10.75 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Actin has been a major target for structural studies in biology since F. B. Straub discovered it in 1942.1 This is probably because actin is one of the most abundant proteins in the eukaryotic cell as well as a key player in many physiological events, ranging from genetics to motility.
    Advances in Experimental Medicine and Biology 02/2007; 592:385-401. DOI:10.1007/978-4-431-38453-3_32 · 2.01 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: In 2003, we published the crystal structures of the core domains of human cardiac muscle troponin (Takeda et al., 2003). Thus, for the first time we were able to visualize the architecture of the molecule; and to see how the three components (TnC, TnI and TnT) fold together to form the troponin molecule. Moreover, our molecular switch mechanism was confirmed, which was previously proposed (Vassylyev et al., 1998) based on the crystal structure of a much smaller complex (the full length TnC in complex with TnI (1–47), a short N-terminal fragment of TnI, both from rabbit skeletal muscle troponin). Namely, a C-terminal TnI segment (117–126 in the rabbit skeletal troponin sequence), directly downstream from the “inhibitory region” (104–115), forms an amphipathic α-helix and interacts with the hydrophobic pocket of the TnC N-lobe in a [Ca2+]-dependent manner. This binding removes the inhi-bitory region from actin-tropomyosin, and thereby relieves the inhibitory action of TnI.
    Advances in Experimental Medicine and Biology 02/2007; 592:37-46. DOI:10.1007/978-4-431-38453-3_5 · 2.01 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Knowledge of the phalloidin binding position in F-actin and the relevant understanding of the mechanism of F-actin stabilization would help to define the structural characteristics of the F-actin filament. To determine the position of bound phalloidin experimentally, x-ray fiber diffraction data were obtained from well-oriented sols of F-actin and the phalloidin-F-actin complex. The differences in the layer-line intensity distributions, which were clearly observed even at low resolution (8 A), produced well-resolved peaks corresponding to interphalloidin vectors in the cylindrically averaged difference-Patterson map, from which the radial binding position was determined to be approximately 10 A from the filament axis. Then, the azimuthal and axial positions were determined by single isomorphous replacement phasing and a cross-Patterson map in radial projection to be approximately 84 degrees and 0.5 A relative to the actin mass center. The refined position was close to the position found by prior researchers. The position of rhodamine attached to phalloidin in the rhodamine-phalloidin-F-actin complex was also determined, in which the conjugated Leu(OH)(7) residue was found to face the outside of the filament. The position and orientation of the bound phalloidin so determined explain the increase in the interactions between long-pitch strands of F-actin and would also account for the inhibition of phosphate release, which might also contribute to the F-actin stabilization. The method of analysis developed in this study is applicable for the determination of binding positions of other drugs, such as jasplakinolide and dolastatin 11.
    Biophysical Journal 05/2005; 88(4):2727-36. DOI:10.1529/biophysj.104.047753 · 3.83 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Dolastatin 11, a drug isolated from the Indian Ocean sea hare Dolabella auricularia, arrests cytokinesis in vivo and increases the amount of F-actin to stabilize F-actin in vitro, like phalloidin and jasplakinolide. However, according to the previous biochemical study, the binding of dolastatin 11 to F-actin does not compete with that of phalloidin, suggesting that the binding sites are different. To understand the mechanism of F-actin stabilization by dolastatin 11, we determined the position of bound dolastatin 11 in F-actin using the X-ray fiber diffraction from oriented filament sols. Our analysis shows that the position of dolastatin 11 is clearly different from that of phalloidin. However, these bound drugs are present in the gap between the two long-pitch F-actin strands in a similar way. The result suggests that the connection between the two long-pitch F-actin strands might be a key for the control of F-actin stabilization.
    Journal of Molecular Biology 05/2003; 328(2):319-24. DOI:10.1016/S0022-2836(03)00306-1 · 3.96 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Lowering pH or raising salt concentration stabilizes the F-actin structure by increasing the free energy change associated with its polymerization. To understand the F-actin stabilization mechanism, we studied the effect of pH, salt concentration, and cation species on the F-actin structure. X-ray fiber diffraction patterns recorded from highly ordered F-actin sols at high density enabled us to detect minute changes of diffraction intensities and to precisely determine the helical parameters. F-actin in a solution containing 30 mM NaCl at pH 8 was taken as the control. F-actin at pH 8, 30 to 90 mM NaCl or 30 mM KCl showed a helical symmetry of 2.161 subunits per turn of the 1-start helix (12.968 subunits/6 turns). Lowering pH from 8 to 6 or replacing NaCl by LiCl altered the helical symmetry to 2.159 subunits per turn (12.952/6). The diffraction intensity associated with the 27-A meridional layer-line increased as the pH decreased but decreased as the NaCl concentration increased. None of the solvent conditions tested gave rise to significant changes in the pitch of the left-handed 1-start helix (approximately 59.8 A). The present results indicate that the two factors that stabilize F-actin, relatively low pH and high salt concentration, have distinct effects on the F-actin structure. Possible mechanisms will be discussed to understand how F-actin is stabilized under these conditions.
    Biophysical Journal 03/2001; 80(2):841-51. DOI:10.1016/S0006-3495(01)76063-8 · 3.83 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: We examined factors that affect the filament orientation in F-actin sols to prepare highly well-oriented liquid crystalline sols suitable for x-ray fiber diffraction structure analysis. Filamentous particles such as F-actin spontaneously align with one another when concentrated above a certain threshold concentration. This alignment is attributed to the excluded volume effect of the particles. In trying to improve the orientation of F-actin sols, we focused on the excluded volume to see how it affects the alignment. The achievable orientation was sensitive to the ionic strength of the solvent; the filaments were better oriented at lower ionic strengths, where the effective diameter of the filament is relatively large. Sols of longer filaments were better oriented than those of shorter filaments at the same concentration, but the best achievable orientation was limited, probably because of the filament flexibility. The best strategy for making well-oriented F-actin sols is therefore to concentrate F-actin filaments of relatively short length (<1 micrometer) by slow centrifugation in a low-ionic-strength solvent (<30 mM).
    Biophysical Journal 01/1999; 75(6):2672-81. DOI:10.1016/S0006-3495(98)77712-4 · 3.83 Impact Factor

Publication Stats

664 Citations
131.08 Total Impact Points


  • 2009–2013
    • RIKEN
      Вако, Saitama, Japan
  • 2012
    • Aizawa Hospital
      Honjō, Saitama, Japan
  • 2010
    • Nagoya University
      • Department of Biological Science
      Nagoya, Aichi, Japan
  • 2007–2009
    • SPring-8
      Saitama, Saitama, Japan
  • 2003–2005
    • Max Planck Institute for Medical Research
      Heidelburg, Baden-Württemberg, Germany