Two C-terminal ankyrin repeats form the minimal stable unit of the ankyrin repeat protein p18INK4c

  • Petr Sklenovský
  • Pavel Banáš
  • Michal Otyepka
Original Paper


Ankyrin repeat proteins (ARPs) appear to be abundant in organisms from all phyla, and play critical regulatory roles, mediating specific interactions with target biomolecules and thus ordering the sequence of events in diverse cellular processes. ARPs possess a non-globular scaffold consisting of repeating motifs named ankyrin (ANK) repeats, which stack on each other. The modular architecture of ARPs provides a new paradigm for understanding protein stability and folding mechanisms. In the present study, the stability of various C-terminal fragments of the ARP p18INK4c was investigated by all-atomic 450 ns molecular dynamics (MD) simulations in explicit water solvent. Only motifs with at least two ANK repeats made stable systems in the available timescale. All smaller fragments were unstable, readily losing their native fold and α-helical content. Since each non-terminal ANK repeat has two hydrophobic sides, we may hypothesize that at least one hydrophobic side must be fully covered and shielded from the water as a necessary, but not sufficient, condition to maintain ANK repeat stability. Consequently, at least two ANK repeats are required to make a stable ARP.


Structure of the p18INK4c protein (PDB entry 1IHB, chain B), which is a member of the cyclin-dependent kinase inhibitor (INK) tumor suppressor family with five ankyrin (ANK) repeat modules. The figure was generated by PyMol


Ankyrin repeat p18INK4c Minimal stable unit Fragmentation Molecular dynamics 



Support through the MSMT (Ministry of Youths, Sports and Education, Czech Republic) grants LC512 and MSM6198959216 is gratefully acknowledged. We thank Sees-Editing, Ltd., (UK) for language revision.

Supplementary material

894_2008_300_MOESM1_ESM.pdf (403 kb)
ESM 1 (PDF 402 kb)


  1. 1.
    Sedgwick SG, Smerdon SJ (1999) Trends Biochem Sci 24:311–316CrossRefGoogle Scholar
  2. 2.
    Mohler PJ, Gramolini AO, Bennett V (2002) J Cell Sci 115:1565–1566Google Scholar
  3. 3.
    Serrano M, Hannon GJ, Beach D (1993) Nature 366:704–707CrossRefGoogle Scholar
  4. 4.
    Mosavi LK, Williams S, Peng ZY (2002) J Mol Biol 320:165–170CrossRefGoogle Scholar
  5. 5.
    Walker RG, Willingham AT, Zuker CS (2000) Science 287:2229–2234CrossRefGoogle Scholar
  6. 6.
    Michaely P, Bennett V (1993) J Biol Chem 268:22703–22709Google Scholar
  7. 7.
    Zhang B, Peng ZY (2000) J Mol Biol 299:1121–1132CrossRefGoogle Scholar
  8. 8.
    Mosavi LK, Minor DL, Peng ZY (2002) Proc Nat Acad Sci USA 99:16029–16034CrossRefGoogle Scholar
  9. 9.
    Tripp KW, Barrick D (2007) J Mol Biol 365:1187–1200CrossRefGoogle Scholar
  10. 10.
    Ferreiro DU, Cervantes CF, Truhlar SME, Cho SS, Wolynes PG, Komives EA (2007) J Mol Biol 365:1201–1216CrossRefGoogle Scholar
  11. 11.
    Binz HK, Kohl A, Pluckthun A, Grutter MG (2006) Proteins: Struct Funct Bioinf 65:280–284CrossRefGoogle Scholar
  12. 12.
    Binz HK, Amstutz P, Kohl A, Stumpp MT, Briand C, Forrer P, Grutter MG, Pluckthun A (2004) Nat Biotechnol 22:575–582CrossRefGoogle Scholar
  13. 13.
    Binz HK, Stumpp MT, Forrer P, Amstutz P, Pluckthun A (2003) J Mol Biol 332:489–503CrossRefGoogle Scholar
  14. 14.
    Devi VS, Binz HK, Stumpp MT, Pluckthun A, Bosshard HR, Jelesarov I (2004) Protein Sci 13:2864–2870CrossRefGoogle Scholar
  15. 15.
    Zahnd C, Wyler E, Schwenk JM, Steiner D, Lawrence MC, McKern NM, Pecorari F, Ward CW, Joos TO, Pluckthun A (2007) J Mol Biol 369:1015–1028CrossRefGoogle Scholar
  16. 16.
    Kohl A, Binz HK, Forrer P, Stumpp MT, Pluckthun A, Grutter MG (2003) Proc Nat Acad Sci USA 100:1700–1705CrossRefGoogle Scholar
  17. 17.
    Mosavi LK, Peng ZY (2003) Protein Eng 16:739–745CrossRefGoogle Scholar
  18. 18.
    Main ERG, Lowe AR, Mochrie SGJ, Jackson SE, Regan L (2005) Curr Opin Struct Biol 15:464–471CrossRefGoogle Scholar
  19. 19.
    Ferreiro DU, Cho SS, Komives EA, Wolynes PG (2005) J Mol Biol 354:679–692CrossRefGoogle Scholar
  20. 20.
    Venkataramani R, Swaminathan K, Marmorstein R (1998) Nat Struct Biol 5:74–81CrossRefGoogle Scholar
  21. 21.
    Pearlman DA, Case DA, Caldwell JW, Ross WS, Cheatham TE, Debolt S, Ferguson D, Seibel G, Kollman P (1995) Comput Phys Commun 91:1–41CrossRefGoogle Scholar
  22. 22.
    Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA (1995) J Am Chem Soc 117:5179–5197CrossRefGoogle Scholar
  23. 23.
    Wang JM, Cieplak P, Kollman PA (2000) J Comput Chem 21:1049–1074CrossRefGoogle Scholar
  24. 24.
    Bartova I, Otyepka M, Kriz Z, Koca J (2004) Protein Sci 13:1449–1457CrossRefGoogle Scholar
  25. 25.
    Otyepka M, Bartova I, Kriz Z, Koca J (2006) J Biol Chem 281:7271–7281CrossRefGoogle Scholar
  26. 26.
    Bartova I, Otyepka M, Kriz Z, Koca J (2005) Protein Sci 14:445–451CrossRefGoogle Scholar
  27. 27.
    Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) J Chem Phys 79:926–935CrossRefGoogle Scholar
  28. 28.
    Kabsch W, Sander C (1983) Biopolymers 22:2577–2637CrossRefGoogle Scholar
  29. 29.
    Du DG, Gai F (2006) Biochemistry 45:13131–13139CrossRefGoogle Scholar
  30. 30.
    DeLano WL (2002) DeLano Scientific.

Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  • Petr Sklenovský
    • 1
  • Pavel Banáš
    • 1
  • Michal Otyepka
    • 1
  1. 1.Department of Physical Chemistry and Center for Biomolecules and Complex Molecular Systems, Faculty of SciencePalacký UniversityOlomoucCzech Republic

Personalised recommendations