Skip to main content
SpringerLink
Log in

Putative binding modes of Ku70-SAP domain with double strand DNA: a molecular modeling study

  • Original Paper
  • Published:
Journal of Molecular Modeling Aims and scope Submit manuscript

Abstract

The channel structure of the Ku protein elegantly reveals the mechanistic basis of sequence-independent DNA-end binding, which is essential to genome integrity after exposure to ionizing radiation or in V(D)J recombination. However, contradicting evidence indicates that this protein is also involved in the regulation of gene expression and in other regulatory processes with intact chromosomes. This computational study predicts that a putative DNA binding domain of this protein, the SAP domain, can form DNA-bound complexes with relatively high affinities (ΔG ≈ -20 kcal mol-1). The binding modes are searched by low frequency vibration modes driven by the fully flexible docking method while binding affinities are calculated by the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method. We find this well defined 5 kDa domain with a helix-extended loop-helix structure is suitable to form favorable electrostatic and hydrophobic interactions with either the major groove or the minor groove of DNA. The calculation also reveals the sequence specified binding preference which may relate to the observed pause sites when Ku translocates along DNA and the perplex binding of Ku with circular DNA.

Ku70-SAP domain binds with DNA at the major and the minor grooves

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

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7

Similar content being viewed by others

References

  1. Downs JA, Jacksons SP (2004) A means to a DNA end: the many roles of Ku. Nature Rev Mol Cell Biol 5:367–378

    Article  CAS  Google Scholar 

  2. Anderson CW, Carter TH (1996) The DNA-activated protein kinase-DNA-PK. In: Jessberger R, Lieber MR (eds) Molecular Analysis of DNA Rearrangements in the Immune System. Springer, Heidelberg, pp 91–112

    Google Scholar 

  3. Fewell JW, Kuff EL (1996) Intracellular redistribution of Ku immunoreactivity in response to cell–cell contact and growth modulating components in the medium. J Cell Sci 109:1937–1946

    CAS  Google Scholar 

  4. Mahaney BL, Meek K, Lees-Miller SP (2009) Repair of ionizing radiation-induced DNA double-strand breaks by non-homologous end-joining. Biochem J 417:639–650

    Article  CAS  Google Scholar 

  5. Weterings E, Chen DJ (2008) The endless tale of non-homologous end-joining. Cell Res 18:114–124

    Article  CAS  Google Scholar 

  6. Polo SE (2011) Jackson SP (2011) Dynamics of DNA damage response proteins at DNA breaks: a focus on protein modifications. Genes Dev 25:409–433

    Article  CAS  Google Scholar 

  7. Lieber MR (2008) The mechanism of human nonhomologous DNA end joining. J Biol Chem 283:1–5

    Article  CAS  Google Scholar 

  8. Lieber MR, Lu H, Gu J, Schwarz K (2008) Flexibility in the order of action and in the enzymology of the nuclease, polymerases, and ligase of vertebrate non-homologous DNA end joining: relevance to cancer, aging, and the immune system. Cell Res 18:125–133

    Article  CAS  Google Scholar 

  9. Walker JR, Corpina RA, Goldberg J (2001) Structure of the Ku heterodimer bound to DNA and its implications for double-strand break repair. Nature 412:607–614

    Article  CAS  Google Scholar 

  10. Rivera-Calzada A, Spagnolo L, Pearl LH, Llorca O (2007) Structural model of full-length human Ku70-Ku80 heterodimer and its recognition of DNA and DNA-PKcs 8:56–62

  11. Aravind L, Koonin EV (2000) SAP — a putative DNA-binding motif involved in chromosomal organization. Trends Biochem Sci 25:112–114

    Article  CAS  Google Scholar 

  12. Wang J, Dong X, Reeves WH (1998) A model for ku heterodimer assembly and interaction with DNA. J Biol Chem 273:31068–31074

    Article  CAS  Google Scholar 

  13. Zhang Z, Zhu L, Lin D et al. (2001) The three-dimensional structure of the C-terminal DNA-binding domain of human Ku70. J Biol Chem 276:38231–38236

    CAS  Google Scholar 

  14. Dynan WS, Yoo S (1998) Interaction of Ku protein and DNA-dependent protein kinase catalytic subunit with nucleic acids. Nucleic Acids Res 26:1551–1559

    Article  CAS  Google Scholar 

  15. Cucinotta FA, Pluth JM, Anderson JA et al. (2008) Biochemical kinetics model of DSB repair and induction of gamma-h2ax foci by non-homologous end joining. Radiat Res 169:214–222

    Article  CAS  Google Scholar 

  16. Durante M, Cucinotta FA (2008) Heavy ion carcinogenesis and human space exploration. Nat Rev Cancer 8:465–472

    Article  CAS  Google Scholar 

  17. Becker OM, MacKerell AD Jr, Roux B, Watanabe M (eds) (2001) Computational Biochemistry and Biophysics. Dekker, New York

    Google Scholar 

  18. Gilson MK, Zhou HX (2007) Calculation of protein-ligand binding affinities. Annu Rev Biophys Biomol Struct 36:21–42

    Article  CAS  Google Scholar 

  19. Smith JA, Tsui VT, Chazin WJ, Case DA (to be published) NMR structure of the palindromic dna decamer d(GCGTTAACGC)2

  20. Case DA, Darden TA, Cheatham TE III et al. (2006) AMBER 9. University of California, San Francisco

    Google Scholar 

  21. Baker NA, Sept D, Joseph S et al. (2001) Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci USA 98:10037–10041

    Article  CAS  Google Scholar 

  22. Kolossváry I, Guida WC (1996) Low mode search. An efficient, automated computational method for conformational analysis: Application to cyclic and acyclic alkanes and cyclic peptides. Am Chem Soc 118:5011–5019

    Article  Google Scholar 

  23. Kolossváry I, Guida WC (1999) Low-mode conformatinoal search elucidated: application to C39H80 and flexible docking of 9-deazaguanine inhibitors into PNP. J Comput Chem 20:1671–1684

    Article  Google Scholar 

  24. Kolossváry I, Keserü GM (2001) Hessian-free low-mode conformational search for large-scale protein loop optimization: Application to c-jun Nterminal kinase JNK3. J Comput Chem 22:21–30

    Article  Google Scholar 

  25. Keserü GM, Kolossváry I (2001) Fully flexible low-mode docking: Application to induced fit in HIV integrase. J Am Chem Soc 123:12708–12709

    Article  Google Scholar 

  26. Hornak V, Abel R, Okur A et al. (2006) Comparison of multiple amber force fields and development of improved protein backbone parameters. Proteins 65:712–725

    Article  CAS  Google Scholar 

  27. Onufriev A, Bashford D, Case DA (2004) Exploring native states and large-scale conformational changes with a modified Generalized Born model. Proteins 55:383–394

    Article  CAS  Google Scholar 

  28. Liu DC, Nocedal J (1989) On the limited memory BFGS method for large scale optimization. Math Prog 45:503–528

    Article  Google Scholar 

  29. Srinivasan J, Cheatham TE III, Cieplak P et al. (1998) Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate-DNA Helices. J Am Chem Soc 120:9401–9409

    Article  CAS  Google Scholar 

  30. Sharp KA, Honig B (1990) Electrostatic interactions in macromolecules - theory and applications. Annu Rev Biophys Biophys Chem 19:301–332

    Article  CAS  Google Scholar 

  31. Sharp KA, Honig B (1990) Calculating total electrostatic energies with the nonlinear Poisson-Boltzmann equation. J Phys Chem 94:7684–7692

    Article  CAS  Google Scholar 

  32. Cheatham TE III, Srinivasan J, Case DA, Kollman PA (1998) Molecular dynamics and continuum solvent studies of the stability of polyG-polyC and polyA-polyT DNA duplexes in solution. J Biomol Struct Dynam 16:265–280

    CAS  Google Scholar 

  33. van Dijk M, van Dijk ADJ, Hsu V et al. (2006) Information-driven protein-DNA docking using HADDOCK: it is a matter of flexibility. Nucleic Acids Res 34:3317–3325

    Article  Google Scholar 

  34. Gohlke H, Kiel C, Case DA (2003) Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes. J Mol Biol 330:891–913

    Article  CAS  Google Scholar 

  35. Misra VK, Honig B (1995) On the magnitude of the electrostatic contribution to ligand-DNA. Proc Nat Acad Sci USA 92:4691–4695

    Article  CAS  Google Scholar 

  36. Singh SB, Kollman PA (1999) Calculating the absolute free energy of association of netropsin and DNA. J Am Chem Soc 121:3267–3271

    Article  CAS  Google Scholar 

  37. Shaikh SA, Ahmed SR, Jayaram B (2004) A molecular thermodynamic view of DNA–drug interactions: a case study of 25 minor-groove binders. Arch Biochem Biophys 429:81–99

    Article  CAS  Google Scholar 

  38. Luscombe NM, Austin SE, Berman HM, Thornton JM (2000) An overview of the structures of protein-DNA complexes. Genome Biol 1:1–37

    Article  Google Scholar 

  39. Kochoyan M, Leroy JL (1995) Hydration and solution structure of nucleic acids. Curr Opin Struct Biol 5:329–333

    Article  CAS  Google Scholar 

  40. Berman HM (1991) Hydration of DNA. Curr Opin Struct Biol 1:423–427

    Article  CAS  Google Scholar 

  41. Jayaram B, Jain T (2004) The role of water in protein-dna recognition. Annu Rev Biophys Biomol Struct 33343–361

Download references

Acknowledgments

The authors thank Dr. István Kolossváry for kind help on LMOD calculations. Part of computations was performed on computers at TLC2 of the University of Houston. Funding for this study was provided by the NASA Space Radiation Program, Risk Assessment Project.

Author information

Authors and Affiliations

  1. Division of Space Life Sciences, Universities Space Research Association, Houston, TX, 77058, USA

    Shaowen Hu

  2. Lawrence Berkeley National Laboratory, Life Sciences Division, One Cyclotron Road, Building 74, Berkeley, CA, 94720, USA

    Janice M. Pluth

  3. NASA, Lyndon B. Johnson Space Center, 2101 NASA Parkway, Houston, TX, 77058, USA

    Francis A. Cucinotta

Authors
  1. Shaowen Hu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Janice M. Pluth
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Francis A. Cucinotta
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Shaowen Hu.

Supplementary material available

Below is the link to the electronic supplementary material.

ESM 1

(DOC 251 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Hu, S., Pluth, J.M. & Cucinotta, F.A. Putative binding modes of Ku70-SAP domain with double strand DNA: a molecular modeling study. J Mol Model 18, 2163–2174 (2012). https://doi.org/10.1007/s00894-011-1234-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00894-011-1234-x

Keywords

Search

Navigation