Molecular Biology

, Volume 52, Issue 1, pp 118–135 | Cite as

Search for Functionally Significant Motifs and Amino Acid Residues of Actin

  • T. S. Tikhomirova
  • R. S. Ievlev
  • M. Yu. Suvorina
  • L. G. Bobyleva
  • I. M. Vikhlyantsev
  • A. K. Surin
  • O. V. Galzitskaya


The scientific interest to the structural and functional properties of actin is determined by its abundance in cells. Being an important component of the cytoskeleton, actin is involved in many protein-protein interactions. Using crystal structures and molecular models, we have mapped the amino acid residues that are involved in these interactions and form the ATP-binding site of the actin monomer. Moreover, using mass spectrometry and high-performance liquid chromatography methods, we have discovered the regions of the amino acid sequence of actin that form the core of the actin fibril. According to the bioinformatic analysis, these regions are amyloidogenic and are located in the C-terminal region and in the hinge between the first and third subdomains. The data obtained are applicable to chordate actin, because multiple alignment revealed highly conserved amino acid sequences. In turn, the comparison of the chordate actin with the bacterial homologs showed the presence of numerous amino acid substitutions and insertions.


actin multiple alignment fibril actin mass spectrometry 



actin-binding proteins


high-performance liquid chromatography


normalized conservation index


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Dominguez R., Holmes K.C. 2011. Actin structure and function. Annu. Rev. Biophys. 40, 169–186.CrossRefPubMedPubMedCentralGoogle Scholar
  2. 2.
    Popp D., Narita A., Oda T., et al. 2008. Molecular structure of the ParM polymer and the mechanism leading to its nucleotide-driven dynamic instability. EMBO J. 27 (3), 570–579.CrossRefPubMedPubMedCentralGoogle Scholar
  3. 3.
    Colavin A., Hsin J., Huang K.C. 2014. Effects of polymerization and nucleotide identity on the conformational dynamics of the bacterial actin homolog MreB. Proc. Natl. Acad. Sci. U. S. A. 111 (9)}, 3585–3590.CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Barkó S., Szatmári D., Bódis E., et al. 2016. Largescale purification and in vitro characterization of the assembly of MreB from Leptospira interrogans. Biochim. Biophys. Acta. 1860 (9), 1942–1952.CrossRefPubMedGoogle Scholar
  5. 5.
    Oda T., Iwasa M., Aihara T., et al. 2009. The nature of the globular- to fibrous-actin transition. Nature. 457 (7228), 441–445.CrossRefPubMedGoogle Scholar
  6. 6.
    Page R., Lindberg U., Schutt C.E. 1998. Domain motions in actin1. J. Mol. Biol. 280 (3), 463–474.CrossRefPubMedGoogle Scholar
  7. 7.
    Kabsch W., Mannherz H.G., Suck D., et al. 1990. Atomic structure of the actin: DNase I complex. Nature. 347 (6288), 37.44.CrossRefPubMedGoogle Scholar
  8. 8.
    Nyman T., Schüler H., Korenbaum E., et al. 2002. The role of MeH73 in actin polymerization and ATP hydrolysis. J. Mol. Biol. 317 (4), 577–58CrossRefPubMedGoogle Scholar
  9. 9.
    Dominguez R. 2004. Actin-binding proteins: A unifying hypothesis. Trends Biochem. Sci. 29 (11), 572–578.CrossRefPubMedGoogle Scholar
  10. 10.
    Rould M. A., Wan Q., Joel P.B., et al. 2006. Crystal structures of expressed non-polymerizable monomeric actin in the ADP and ATP states. J. Biol. Chem. 281 (42), 31909–31919.CrossRefPubMedGoogle Scholar
  11. 11.
    Nair U.B., Joel P.B., Wan Q., et al. 2008. Crystal structures of monomeric actin bound to cytochalasin D. J. Mol. Biol. 384 (4), 848–864.CrossRefPubMedPubMedCentralGoogle Scholar
  12. 12.
    Chik J.K., Lindberg U., Schutt C.E. 1996. The structure of an open state of β-actin at 2.65 Å resolution. J. Mol. Biol. 263 (4), 607–623.CrossRefPubMedGoogle Scholar
  13. 13.
    Verboven C., Bogaerts I., Waelkens E., et al. 2003. Actin-DBP: The perfect structural fit? Acta Crystallogr. D: Biol. Crystallogr. 59 (2), 263–273.CrossRefGoogle Scholar
  14. 14.
    Chereau D., Kerff F., Graceffa P., et al. 2005. Actinbound structures of Wiskott-Aldrich syndrome protein (WASP)-homology domain 2 and the implications for filament assembly. Proc. Natl. Acad. Sci. U. S. A. 102 (46), 16644–16649.CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Nag S., Ma Q., Wang H., et al. 2009. Ca2+ binding by domain 2 plays a critical role in the activation and stabilization of gelsolin. Proc. Natl. Acad. Sci. U. S. A. 106 (33), 13713–13718.CrossRefPubMedPubMedCentralGoogle Scholar
  16. 16.
    Chen X., Ni F., Kondrashkina E., et al. 2015. Mechanisms of leiomodin 2-mediated regulation of actin filament in muscle cells. Proc. Natl. Acad. Sci. U. S. A. 112 (41), 12687–12692.CrossRefPubMedPubMedCentralGoogle Scholar
  17. 17.
    Chen X., Ni F., Tian X., et al. 2013. Structural basis of actin filament nucleation by tandem W domains. Cell Rep. 3 (6), 1910–1920.CrossRefPubMedPubMedCentralGoogle Scholar
  18. 18.
    Zahm J.A., Padrick S.B., Chen Z., et al. 2013. Structure of a filament-like actin trimer bound to the bacterial effector VopL. Cell. 155 (2), 423.434.CrossRefPubMedPubMedCentralGoogle Scholar
  19. 19.
    von der Ecken J., Heissler S.M., Pathan-Chhatbar S., et al. 2016. Cryo-EM structure of a human cytoplasmic actomyosin complex at near-atomic resolution. Nature. 534 (7609), 724–728.CrossRefPubMedGoogle Scholar
  20. 20.
    Behrmann E., Müller M., Penczek P.A., et al. 2012. Structure of the rigor actin.tropomyosin.myosin complex. Cell. 150 (2), 327–338.CrossRefPubMedPubMedCentralGoogle Scholar
  21. 21.
    Kim L.Y., Thompson P.M., Lee H.T., et al. 2016. The structural basis of actin organization by vinculin and metavinculin. J. Mol. Biol. 428 (1), 10–25.CrossRefPubMedGoogle Scholar
  22. 22.
    Galkin V.E., Orlova A., Kudryashov D.S., et al. 2011. Remodeling of actin filaments by ADF/cofilin proteins. Proc. Natl. Acad. Sci. U. S. A. 108 (51), 20568–20572.CrossRefPubMedPubMedCentralGoogle Scholar
  23. 23.
    Galkin V.E., Orlova A., Cherepanova O., et al. 2008. High-resolution cryo-EM structure of the F-actinfimbrin/ plastin ABD2 complex. Proc. Natl. Acad. Sci. U. S. A. 105 (5), 1494–1498.CrossRefPubMedPubMedCentralGoogle Scholar
  24. 24.
    Sievers F., Higgins D.G. 2014. Clustal Omega, accurate alignment of very large numbers of sequences. Methods Mol. Biol. Clifton NJ. 1079, 105–116.CrossRefGoogle Scholar
  25. 25.
    Manning J.R., Jefferson E.R., Barton G.J. 2008. The contrasting properties of conservation and correlated phylogeny in protein functional residue prediction. BMC Bioinform. 9, 51.CrossRefGoogle Scholar
  26. 26.
    Trott O., Olson A.J. 2010. AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J. Comput. Chem. 31 (2), 455–461.PubMedPubMedCentralGoogle Scholar
  27. 27.
    Feuer G., Molnar F. 1948. Studies on the composition and polymerization of actin. Hung. Acta Physiol. 1 (4–5), 150–163.PubMedGoogle Scholar
  28. 28.
    Pardee J.D., Spudich J.A. 1982. Purification of muscle actin. Methods Cell Biol. 24, 271–289.CrossRefPubMedGoogle Scholar
  29. 29.
    Offer G., Moos C., Starr R. 1973. A new protein of the thick filaments of vertebrate skeletal myofibrils. Extractions, purification and characterization. J. Mol. Biol. 74 (4), 653–676.CrossRefPubMedGoogle Scholar
  30. 30.
    Rees M.K., Young M. 1967. Studies on the isolation and molecular properties of homogeneous globular actin. Evidence for a single polypeptide chain structure. J. Biol. Chem. 242 (19), 4449–4458.PubMedGoogle Scholar
  31. 31.
    Surin A.K., Grigorashvili E.I., Suvorina M.Y., et al. 2016. Determination of regions involved in amyloid fibril formation for Aβ(1–40) peptide. Biochemistry (Moscow). 81 (7), 762–769. doi 10.1134/S0006297916070130CrossRefGoogle Scholar
  32. 32.
    Lobanov M.Y., Sokolovskiy I.V., Galzitskaya O.V. 2013. IsUnstruct: Prediction of the residue status to be ordered or disordered in the protein chain by a method based on the Ising model. J. Biomol. Struct. Dyn. 31 (10), 1034–1043.CrossRefPubMedGoogle Scholar
  33. 33.
    Galzitskaya O.V., Garbuzynskiy S.O., Lobanov M.Y. 2006. FoldUnfold: Web server for the prediction of disordered regions in protein chain. Bioinformatics. 22 (23), 2948–2949.CrossRefPubMedGoogle Scholar
  34. 34.
    Garbuzynskiy S.O., Lobanov M.Y., Galzitskaya O.V. 2010. FoldAmyloid: A method of prediction of amyloidogenic regions from protein sequence. Bioinformatics. 26 (3), 326–332.CrossRefPubMedGoogle Scholar
  35. 35.
    Skvortsov V.S., Alekseychuk N.N., Khudyakov D.V., et al. 2015. pIPredict: A computer tool for predicting isoelectric points of peptides and proteins. Biomed. Khim. 61 (1), 83–91.CrossRefPubMedGoogle Scholar
  36. 36.
    Yao X., Grade S., Wriggers W., et al. 1999. His73, often methylated, is an important structural determinant for actin A mutagenic analysis of His73 of yeast actin. J. Biol. Chem. 274 (52), 37443–37449.CrossRefPubMedGoogle Scholar
  37. 37.
    D′Amico A., Graziano C., Pacileo G., et al. 2006. Fatal hypertrophic cardiomyopathy and nemaline myopathy associated with ACTA1 K336E mutation. Neuromuscul. Disord. 16 (9–10)}, 548–552.CrossRefPubMedGoogle Scholar
  38. 38.
    Marston S., Memo M., Messer A., et al. 2013. Mutations in repeating structural motifs of tropomyosin cause gain of function in skeletal muscle myopathy patients. Hum. Mol. Genet. 22 (24), 4978–4987CrossRefPubMedPubMedCentralGoogle Scholar
  39. 39.
    Golji J., Mofrad M.R.K. 2013. The interaction of vinculin with actin. PLoS Comput. Biol. 9 (4), e100299CrossRefPubMedPubMedCentralGoogle Scholar
  40. 40.
    Wong D.Y., Sept D. 2011. The interaction of cofilin with the actin filament. J. Mol. Biol. 413 (1), 97–105.CrossRefPubMedPubMedCentralGoogle Scholar
  41. 41.
    Vorobiev S., Strokopytov B., Drubin D.G., et al. 2003. The structure of nonvertebrate actin: Implications for the ATP hydrolytic mechanism. Proc. Natl. Acad. Sci. U. S. A. 100 (10), 5760–5765.CrossRefPubMedPubMedCentralGoogle Scholar
  42. 42.
    Wen K.-K., Yao X., Rubenstein P.A. 2002. GTP-yeast actin. J. Biol. Chem. 277 (43), 41101–41109.CrossRefPubMedGoogle Scholar
  43. 43.
    Horowitz S., Trievel R.C. 2012. Carbon-oxygen hydrogen bonding in biological structure and function. J. Biol. Chem. 287 (50), 41576–41582.CrossRefPubMedPubMedCentralGoogle Scholar
  44. 44.
    Ribas J., Cubero E., Luque F.J., Orozco M. 2002. Theoretical study of alkyl-pi and aryl-pi interactions. Reconciling theory and experiment. J. Org. Chem. 67 (20), 7057–7065.CrossRefPubMedGoogle Scholar
  45. 45.
    Gleiter R. 2009. Pi-sigma interactions: Experimental evidence and its consequences for the chemical reactivity of organic compounds. Pure Appl. Chem. 59 (12), 1585–1594.CrossRefGoogle Scholar
  46. 46.
    Sinnokrot M.O., Sherrill C.D. 2004. Substituent effects in pi-pi interactions: Sandwich and T-shaped configurations. J. Am. Chem. Soc. 126 (24), 7690–7697.CrossRefPubMedGoogle Scholar

Copyright information

© Pleiades Publishing, Inc. 2018

Authors and Affiliations

  • T. S. Tikhomirova
    • 1
    • 2
  • R. S. Ievlev
    • 1
  • M. Yu. Suvorina
    • 1
  • L. G. Bobyleva
    • 3
  • I. M. Vikhlyantsev
    • 3
    • 4
  • A. K. Surin
    • 1
    • 5
  • O. V. Galzitskaya
    • 1
  1. 1.Institute of Protein ResearchRussian Academy of SciencePushchino, Moscow oblastRussia
  2. 2.Institute for Biological InstrumentationRussian Academy of SciencePushchino, Moscow oblastRussia
  3. 3.Institute of Theoretical and Experimental BiophysicsRussian Academy of SciencePushchino, Moscow oblastRussia
  4. 4.Pushchino State Institute of Natural SciencePushchino, Moscow oblastRussia
  5. 5.State Research Center for Applied Microbiology and BiotechnologyObolensk, Moscow oblastRussia

Personalised recommendations