Skip to main content

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 592))

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.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

32.7. Refernce

  1. F. B. Straub. Actin, Studies Int. Med. Chem. Univ. Szeged. 2, 3–15 (1942).

    CAS  Google Scholar 

  2. F. Straub, and G. Feuer. Adenosinetriphosphate the functional group of actin, Biochim. Biophys. Acta 4, 455–470 (1950).

    Article  CAS  Google Scholar 

  3. F. Oosawa, S. Asakura, K. Hotta, N. Imai, and T. Ooi. G-F transformation of actin as a fibrous condensation, J. Polymer Sci. 37(3), 323–336 (1959).

    Article  CAS  Google Scholar 

  4. F. Oosawa. Size distribution of protein polymers, J. Theor. Biol. 27(1), 69–86 (1970).

    Article  PubMed  CAS  Google Scholar 

  5. D. T. Woodrum, S. A. Rich, and T. D. Pollard. Evidence for biased bidirectional polymerization of actin filaments using heavy meromyosin prepared by an improved method, J. Cell Biol. 67(1), 231–237 (1975).

    Article  PubMed  CAS  Google Scholar 

  6. H. Kondo, and S. Ishiwata. Uni-directional growth of F-actin, J. Biochem. (Tokyo). 79(1), 159–171 (1976).

    CAS  Google Scholar 

  7. A. Wegner. Head to tail polymerization of actin, J. Mol. Biol. 108(1), 139–150 (1976).

    Article  PubMed  CAS  Google Scholar 

  8. N. Selve, and A. Wegner. Rate of treadmilling of actin filaments in vitro, J. Mol. Biol. 187(4), 627–631 (1986).

    Article  PubMed  CAS  Google Scholar 

  9. M. F. Carlier, D. Pantaloni, and E. D. Korn. Evidence for an ATP cap at the ends of actin filaments and its regulation of the F-actin steady state, J. Biol. Chem. 259(16), 9983–9986 (1984).

    PubMed  CAS  Google Scholar 

  10. M. F. Carlier, D. Pantaloni, and E. D. Korn. The mechanisms of ATP hydrolysis accompanying the polymerization of Mg-actin and Ca-actin, J. Biol. Chem. 262(7), 3052–3059 (1987).

    PubMed  CAS  Google Scholar 

  11. S. Hatano, and F. Oosawa. Extraction of an actin-like protein from the plasmodium of a myxomycete and its interaction with myosin A from rabbit striated muscle, J. Cell. Physiol. 68(2), 197–202 (1966).

    Article  PubMed  CAS  Google Scholar 

  12. S. Hatano, and F. Oosawa. Isolation and characterization of plasmodium actin, Biochim. Biophys. Acta 127(2), 488–498 (1966).

    PubMed  CAS  Google Scholar 

  13. T. D. Pollard, and G. G. Borisy. Cellular motility driven by assembly and disassembly of actin filaments, Cell. 112(4), 453–465 (2003).

    Article  PubMed  CAS  Google Scholar 

  14. S. H. Zigmond. Formin-induced nucleation of actin filaments, Curr. Opin. Cell Biol. 16(1), 99–105 (2004).

    Article  PubMed  CAS  Google Scholar 

  15. W. T. Astbury, S. V. Perry, R. Reed, and L. C. Spark. An electron microscopy and X-ray study of actin., Biochim. Biophys. Acta 1, 379–392 (1947).

    Article  Google Scholar 

  16. C. C. Selby, and R. S. Bear. The structure of actin-rich filaments of muscles according to X-ray diffraction, J. Biophys. Biochem. Cytol. 2(1), 71–85 (1956).

    Article  PubMed  CAS  Google Scholar 

  17. C. Cohen, and J. Hanson. An X-ray diffraction study of F-actin, Biochim. Biophys. Acta 21(1), 177–178 (1956).

    Article  PubMed  CAS  Google Scholar 

  18. F. Oosawa, S. Asakura, and T. Ooi. Physical Chemistry of muscle protein “actin,” Prog. Theor. Phys. Suppl. 17, 14–34 (1961).

    Google Scholar 

  19. F. Oosawa, and M. Kasai. A theory of linear and helical aggregations of macromolecules, J. Mol. Biol. 4, 10–21 (1962).

    PubMed  CAS  Google Scholar 

  20. J. Hanson, and J. Lowy. The structure of F-actin of actin filaments isolated from muscle, J. Mol. Biol. 6, 46–60 (1963).

    CAS  Google Scholar 

  21. D. J. DeRosier, and A. Klug. Reconstruction of three dimensional structure from electron micrographs, Nature 217(5124), 130–134 (1968).

    Article  Google Scholar 

  22. P. B. Moore, H. E. Huxley, and D. J. DeRosier. Three-dimensional reconstruction of F-actin, thin filaments and decorated thin filaments, J. Mol. Biol. 50(2), 279–295 (1970).

    Article  PubMed  CAS  Google Scholar 

  23. A. Bremer, R. C. Millonig, R. Sutterlin, A. Engel, T. D. Pollard, and U. Aebi. The structural basis for the intrinsic disorder of the actin filament: the “lateral slipping” model, J. Cell Biol. 115(3), 689–703 (1991).

    Article  PubMed  CAS  Google Scholar 

  24. E. H. Egelman, N. Francis, and D. J. DeRosier. F-actin is a helix with a random variable twist, Nature 298(5870), 131–135 (1982).

    Article  PubMed  CAS  Google Scholar 

  25. J. Trinick, J. Cooper, J. Seymour, and E. H. Egelman. cryo-electron microscopy and three-dimensional reconstruction of actin filament, J. Microsc. 141 (Pt 3), 349–360 (1986).

    PubMed  CAS  Google Scholar 

  26. R. A. Milligan, M. Whittaker, and D. Safer. Molecular structure of F-actin and location of surface binding sites, Nature 348(6298), 217–221 (1990).

    Article  PubMed  CAS  Google Scholar 

  27. E. H. Egelman. A robust algorithm for the reconstruction of helical filaments using single-particle methods, Ultramicroscopy 85(4), 225–234 (2000).

    Article  PubMed  CAS  Google Scholar 

  28. A. Narita, T. Yasunaga, T. Ishikawa, K. Mayanagi, and T. Wakabayashi. Ca(2+)-induced switching of troponin and tropomyosin on actin filaments as revealed by electron cryo-microscopy, J. Mol. Biol. 308(2), 241–261 (2001).

    Article  PubMed  CAS  Google Scholar 

  29. D. Paul, A. Patwardhan, J. M. Squire, and E. P. Morris. Single particle analysis of filamentous and highly elongated macromolecular assemblies, J. Struct. Biol. 148(2), 236–250 (2004).

    Article  PubMed  CAS  Google Scholar 

  30. E. H. Egelman. Molecular evolution: actin’s long lost relative found, Curr. Biol. 11(24), R1022–R1024 (2001).

    Article  PubMed  CAS  Google Scholar 

  31. W. Kabsch, H. G. Mannherz, D. Suck, E. F. Pai, and K. C. Holmes. Atomic structure of the actin:DNase I complex, Nature 347(6288), 37–44 (1990).

    Article  PubMed  CAS  Google Scholar 

  32. K. C. Holmes, D. Popp, W. Gebhard, and W. Kabsch. Atomic model of the actin filament, Nature 347(6288), 44–49 (1990).

    Article  PubMed  CAS  Google Scholar 

  33. M. Lorenz, D. Popp, and K. C. Holmes. Refinement of the F-actin model against X-ray fiber diffraction data by the use of a directed mutation algorithm, J. Mol. Biol. 234(3), 826–836 (1993).

    Article  PubMed  CAS  Google Scholar 

  34. M. M. Tirion, D. ben-Avraham, M. Lorenz, and K. C. Holmes. Normal modes as refinement parameters for the F-actin model, Biophys. J. 68(1), 5–12 (1995).

    PubMed  CAS  Google Scholar 

  35. K. C. Holmes, I. Angert, F. J. Kull, W. Jahn, and R. R. Schroder. Electron cryo-microscopy shows how strong binding of myosin to actin releases nucleotide, Nature 425(6956), 423–427 (2003).

    Article  PubMed  CAS  Google Scholar 

  36. X. Chen, R. K. Cook, and P. A. Rubenstein. Yeast actin with a mutation in the “hydrophobic plug” between subdomains 3 and 4 (L266D) displays a cold-sensitive polymerization defect, J. Cell Biol. 123(5), 1185–1195 (1993).

    Article  PubMed  CAS  Google Scholar 

  37. R. Musib, G. Wang, L. Geng, and P. A. Rubenstein. Effect of polymerization on the subdomain 3/4 loop of yeast actin, J. Biol. Chem. 277(25), 22699–22709 (2002).

    Article  PubMed  CAS  Google Scholar 

  38. A. Shvetsov, R. Musib, M. Phillips, P. A. Rubenstein, and E. Reisler. Locking the hydrophobic loop 262–274 to G-actin surface by a disulfide bridge prevents filament formation, Biochemistry 41(35), 10787–10793 (2002).

    Article  PubMed  CAS  Google Scholar 

  39. T. Oda. Structural analysis of filamentous macromolecular complexes: in the case of actin filament, Seitai no kagaku 56(6), 581–587 (2005).

    CAS  Google Scholar 

  40. D. S. Kudryashov, M. R. Sawaya, H. Adisetiyo, T. Norcross, G. Hegyi, E. Reisler, and T. O. Yeates. The crystal structure of a cross-linked actin dimer suggests a detailed molecular interface in F-actin, Proc. Natl. Acad. Sci. USA 102(37), 13105–13110 (2005).

    Article  PubMed  CAS  Google Scholar 

  41. H. Gong, V. Hatch, L. Ali, W. Lehman, R. Craig, and L. S. Tobacman. Mini-thin filaments regulated by troponin-tropomyosin, Proc. Natl. Acad. Sci. USA 102(3), 656–661 (2005).

    Article  PubMed  CAS  Google Scholar 

  42. K. C. Holmes. Solving the structure of macromolecular complexes with the help of X-ray fiber diffraction diagrams, J. Struct. Biol. 115(2), 151–158 (1995).

    Article  PubMed  CAS  Google Scholar 

  43. D. L. D. Casper. The radial density distribution in the tobacco mosaic virus particle, Nature 177(4516), 928 (1956).

    Article  Google Scholar 

  44. R. E. Franklin. Location of the ribonucleic acid in the tabacco mosaic virus particles, Nature 177(4516), 928–930 (1956).

    Article  CAS  Google Scholar 

  45. K. C. Holmes, G. J. Stubbs, E. Mandelkow, and U. Gallwitz. structure of tobacco mosaic virus at 6.7 A resolution, Nature 254(5497), 192–196 (1975).

    Article  PubMed  CAS  Google Scholar 

  46. G. Stubbs, S. Warren, and K. Holmes. Structure of RNA and RNA binding site in tobacco mosaic virus from 4-A map calculated from X-ray fibre diagrams, Nature 267(5608), 216–221 (1977).

    Article  PubMed  CAS  Google Scholar 

  47. K. Namba, and G. Stubbs. Structure of tobacco mosaic virus at 3.6 A resolution: implications for assembly, Science 231(4744), 1401–1406 (1986).

    Article  PubMed  CAS  Google Scholar 

  48. K. Namba, R. Pattanayek, and G. Stubbs. Visualization of protein-nucleic acid interactions in a virus. Refined structure of intact tobacco mosaic virus at 2.9 A resolution by X-ray fiber diffraction, J. Mol. Biol. 208(2), 307–325 (1989).

    Article  PubMed  CAS  Google Scholar 

  49. K. Namba, and G. Stubbs. Difference Fourier syntheses in fiber diffraction, Acta Cryst. A43 (Pt 4), 533–539 (1987).

    CAS  Google Scholar 

  50. K. Namba, and G. Stubbs. Solving the phase problem in fiber diffraction. Application to tobacco mosaic virus at 3.6 A resolution, Acta Cryst. A41 (Pt 3), 252–262 (1985).

    CAS  Google Scholar 

  51. V. V. Lednev. Structure and function of the thin filaments of the cross-striated muscle of vertebrates. structural parameters of F-actin, Biofizika 19(1), 116–121 (1974).

    PubMed  CAS  Google Scholar 

  52. D. Popp, V. V. Lednev, and W. Jahn. Methods of preparing well-orientated sols of f-actin containing filaments suitable for X-ray diffraction, J. Mol. Biol. 197(4), 679–684 (1987).

    Article  PubMed  CAS  Google Scholar 

  53. T. Oda, K. Makino, I. Yamashita, K. Namba, and Y. Maeda. Effect of the length and effective diameter of F-actin on the filament orientation in liquid crystalline sols measured by X-ray fiber diffraction, Biophys J. 75(6), 2672–2681 (1998).

    PubMed  CAS  Google Scholar 

  54. I. Yamashita, F. Vonderviszt, Y. Mimori, H. Suzuki, K. Oosawa, and K. Namba. Radial mass analysis of the flagellar filament of Salmonella: implications for the subunit folding, J. Mol. Biol. 253(4), 547–558 (1995).

    Article  PubMed  CAS  Google Scholar 

  55. G. J. Stubbs, and R. Diamond. The phase problem for cylindrically averaged diffraction patterns. Solution by isomorphous replacement and application to tobacco mosaic virus, Acta Cryst. A31 (Pt 6), 709–718 (1975).

    CAS  Google Scholar 

  56. M. F. Smith, and J. P. Langmore. Quantitation of molecular densities by cryo-electron microscopy. Determination of the radial density distribution of tobacco mosaic virus, J. Mol. Biol. 226(3), 763–774 (1992).

    Article  PubMed  CAS  Google Scholar 

  57. Y. Mimori, I. Yamashita, K. Murata, Y. Fujiyoshi, K. Yonekura, C. Toyoshima, and K. Namba. The structure of the R-type straight flagellar filament of Salmonella at 9 A resolution by electron cryomicroscopy, J. Mol. Biol. 249(1), 69–87 (1995).

    Article  PubMed  CAS  Google Scholar 

  58. T. W. Jeng, R. A. Crowther, G. Stubbs, and W. Chiu. Visualization of alpha-helices in tobacco mosaic virus by cryo-electron microscopy, J. Mol. Biol. 205(1), 251–257 (1989).

    Article  PubMed  CAS  Google Scholar 

  59. K. Namba, I. Yamashita, and F. Vonderviszt. Structure of the core and central channel of bacterial flagella, Nature 342(6250), 648–654 (1989).

    Article  PubMed  CAS  Google Scholar 

  60. A. Klug, F. H. Crick, and H. W. Wyckoff. Diffraction by helical structure, Acta Cryst. 11 (Pt 3), 199–213 (1958).

    Article  CAS  Google Scholar 

  61. T. Oda, Z. D. Crane, C. W. Dicus, B. A. Sufi, and R. B. Bates. Dolastatin 11 connects two long-pitch strands in F-actin to stabilize microfilaments, J. Mol. Biol. 328(2), 319–324 (2003).

    Article  PubMed  CAS  Google Scholar 

  62. D. L. D. Casper. The radial density distribution in the tobacco mosaic virus particle, Nature 177(4516),928 (1956).

    Article  Google Scholar 

  63. R. E. Franklin. Location of the ribonucleic acid in the tabacco mosaic virus particles, Nature 177, 928–930 (1956).

    Article  CAS  Google Scholar 

  64. A. Orlova, and E. H. Egelman. A conformational change in the actin subunit can change the flexibility of the actin filament, J. Mol. Biol. 232(2), 334–341 (1993).

    Article  PubMed  CAS  Google Scholar 

  65. N. Go, T. Noguti, and T. Nishikawa. Dynamics of a small globular protein in terms of low-frequency vibrational modes, Proc. Natl. Acad. Sci. USA 80(12), 3696–3700 (1983).

    Article  PubMed  CAS  Google Scholar 

  66. B. Brooks, and M. Karplus. Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor, Proc. Natl. Acad. Sci. USA 80(21), 6571–6575 (1983).

    Article  PubMed  CAS  Google Scholar 

  67. M. M. Tirion. Large amplitude elastic motions in proteins from a single-parameter, atomic analysis, Phys. Rev. Lett. 77(9), 1905–1908 (1996).

    Article  PubMed  CAS  Google Scholar 

  68. I. Bahar, A. R. Atilgan, and B. Erman. Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential, Fold Des. 2(3), 173–181 (1997).

    Article  PubMed  CAS  Google Scholar 

  69. F. Tama, and Y. H. Sanejouand. Conformational change of proteins arising from normal mode calculations, Protein Eng. 14(1), 1–6 (2001).

    Article  PubMed  CAS  Google Scholar 

  70. C. Xu, D. Tobi, and I. Bahar. Allosteric changes in protein structure computed by a simple mechanical model: hemoglobin T<->R2 transition, J. Mol. Biol. 333(1), 153–168 (2003).

    Article  PubMed  CAS  Google Scholar 

  71. R. Diamond. On the use of normal modes in thermal parameter refinement: theory and application to the bovine pancreatic trypsin inhibitor, Acta Crystallogr. A 46 (Pt 6), 425–435 (1990).

    Article  PubMed  Google Scholar 

  72. A. Kidera, and N. Go. Normal mode refinement: crystallographic refinement of protein dynamic structure. I. Theory and test by simulated diffraction data, J. Mol. Biol. 225(2), 457–475 (1992).

    Article  PubMed  CAS  Google Scholar 

  73. Y. Wu, and J. Ma. Refinement of F-actin model against fiber diffraction data by long-range normal modes, Biophys J. 86(1 Pt 1), 116–124 (2004).

    Article  PubMed  CAS  Google Scholar 

  74. F. Tama, M. Valle, J. Frank, and C. L. Brooks, 3rd. Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy, Proc. Natl. Acad. Sci. USA 100(16), 9319–9323 (2003).

    Article  PubMed  CAS  Google Scholar 

  75. H. Wang, and G. Stubbs. Molecular dynamics in refinement against fiber diffraction data, Acta Crystallogr A 49(3), 504–513 (1993).

    Article  PubMed  CAS  Google Scholar 

  76. L. R. Otterbein, P. Graceffa, and R. Dominguez. The crystal structure of uncomplexed actin in the ADP state, Science 293(5530), 708–711 (2001).

    Article  PubMed  CAS  Google Scholar 

  77. J. K. Chik, U. Lindberg, and C. E. Schutt. The structure of an open state of beta-actin at 2.65 A resolution, J. Mol. Biol. 263(4), 607–623 (1996).

    Article  PubMed  CAS  Google Scholar 

  78. C. E. Schutt, J. C. Myslik, M. D. Rozycki, N. C. Goonesekere, and U. Lindberg. The structure of crystalline profilin-beta-actin, Nature 365(6449), 810–816 (1993).

    Article  PubMed  CAS  Google Scholar 

  79. R. Page, U. Lindberg, and C. E. Schutt. Domain motions in actin, J. Mol. Biol. 280(3), 463–474 (1998).

    Article  PubMed  CAS  Google Scholar 

  80. F. van den Ent, J. Moller-Jensen, L. A. Amos, K. Gerdes, and J. Lowe. F-actin-like filaments formed by plasmid segregation protein ParM, EMBO J. 21(24), 6935–6943 (2002).

    Article  PubMed  Google Scholar 

  81. F. van den Ent, L. A. Amos, and J. Lowe. Prokaryotic origin of the actin cytoskeleton, Nature 413(6851), 39–44 (2001).

    Article  PubMed  CAS  Google Scholar 

  82. P. J. Kraulis. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures, J. Appl. Cryst 24(5), 946–950 (1991).

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2007 Springer

About this paper

Cite this paper

Oda, T., Stegmann, H., Schröder, R.R., Namba, K., Maéda, Y. (2007). Modeling of the F-Actin Structure. In: Ebashi, S., Ohtsuki, I. (eds) Regulatory Mechanisms of Striated Muscle Contraction. Advances in Experimental Medicine and Biology, vol 592. Springer, Tokyo. https://doi.org/10.1007/978-4-431-38453-3_32

Download citation

Publish with us

Policies and ethics