Skip to main content
Log in

Electrostatic interactions play an essential role in DNA repair and cold-adaptation of Uracil DNA glycosylase

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

Abstract

Life has adapted to most environments on earth, including low and high temperature niches. The increased catalytic efficiency and thermoliability observed for enzymes from organisms living in constantly cold regions when compared to their mesophilic and thermophilic cousins are poorly understood at the molecular level. Uracil DNA glycosylase (UNG) from cod (cUNG) catalyzes removal of uracil from DNA with an increased kcat and reduced Km relative to its warm-active human (hUNG) counterpart. Specific issues related to DNA repair and substrate binding/recognition (Km) are here investigated by continuum electrostatics calculations, MD simulations and free energy calculations. Continuum electrostatic calculations reveal that cUNG has surface potentials that are more complementary to the DNA potential at and around the catalytic site when compared to hUNG, indicating improved substrate binding. Comparative MD simulations combined with free energy calculations using the molecular mechanics-Poisson Boltzmann surface area (MM-PBSA) method show that large opposing energies are involved when forming the enzyme-substrate complexes. Furthermore, the binding free energies obtained reveal that the Michaelis-Menten complex is more stable for cUNG, primarily due to enhanced electrostatic properties, suggesting that energetic fine-tuning of electrostatics can be utilized for enzymatic temperature adaptation. Energy decomposition pinpoints the residual determinants responsible for this adaptation.

Electrostatic isosurfaces of cod uracil DNA glycosylase in complex with double stranded DNA

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

Access this article

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

Similar content being viewed by others

References

  1. Hochachka PW, Somero GN (1984) Temperature adaptation, in Biochemical adaptations. Princeton University Press, Princeton, NJ, pp 355–449

  2. Fields PA, Somero GN (1998) Proc Natl Acad Sci USA 95:11476–11481

    Article  CAS  Google Scholar 

  3. Georlette D, Damien B, Blaise V, Depiereux E, Uversky VN, Gerday C, Feller G (2003) J Biol Chem 278:37015–37023

    Article  CAS  Google Scholar 

  4. Leiros I, Moe E, Lanes O, Smalås AO, Willassen NP (2003) Acta Crystallogr D Biol Crystallogr 59:1357–1365

    Article  Google Scholar 

  5. Olufsen M, Smalås AO, Moe E, Brandsdal BO (2005) J Biol Chem 280:18042–18048

    Article  CAS  Google Scholar 

  6. Smalås AO, Heimstad ES, Hordvik A, Willassen NP, Male R (1994) Proteins 20:149–166

    Article  Google Scholar 

  7. Brandsdal BO, Heimstad ES, Sylte I, Smalås AO (1999) J Biomol Struct Dyn 17:493–506

    CAS  Google Scholar 

  8. Russell RJM, Gerike U, Danson MJ, Hough DW, Taylor GL (1998) Structure 6:351–361

    Article  CAS  Google Scholar 

  9. Kumar S, Nussinov R (2004) ChemBioChem 5:280–290

    Article  CAS  Google Scholar 

  10. Gorfe AA, Brandsdal BO, Leiros HKS, Helland R, Smalås AO (2000) Proteins 40:207–217

    Article  CAS  Google Scholar 

  11. Brandsdal BO, Smalås AO, Åqvist J (2001) FEBS Lett 499:171–175

    Article  CAS  Google Scholar 

  12. Moe E, Leiros I, Riise EK, Olufsen M, Lanes O, Smalås A, Willassen NP (2004) J Mol Biol 343:1221–1230

    Article  CAS  Google Scholar 

  13. Lindahl T, Nyberg B (1974) Biochemistry 13:3405–3410

    Article  CAS  Google Scholar 

  14. Krokan HE, Standal R, Slupphaug G (1997) Biochem J 325:1–16

    CAS  Google Scholar 

  15. Mol CD, Arvai AS, Slupphaug G, Kavli B, Alseth I, Krokan HE, Tainer JA (1995) Cell 80:869–878

    Article  CAS  Google Scholar 

  16. Savva R, Mcauleyhecht K, Brown T, Pearl L (1995) Nature 373:487–493

    Article  CAS  Google Scholar 

  17. Ravishankar R, Sagar MB, Roy S, Purnapatre K, Handa P, Varshney U, Vijayan M (1998) Nucleic Acids Res 26:4880–4887

    Article  CAS  Google Scholar 

  18. Geoui T, Buisson M, Tarbouriech N, Burmeister WP (2007) J Mol Biol 366:117–131

    Article  CAS  Google Scholar 

  19. Bianchet MA, Seiple LA, Jiang YL, Ichikawa Y, Amzel LM, Stivers JT (2003) Biochemistry 42:12455–12460

    Article  CAS  Google Scholar 

  20. Parikh SS, Mol CD, Slupphaug G, Bharati S, Krokan HE, Tainer JA (1998) EMBO J 17:5214–5226

    Article  CAS  Google Scholar 

  21. Parikh SS, Walcher G, Jones GD, Slupphaug G, Krokan HE, Blackburn GM, Tainer JA (2000) Proc Natl Acad Sci USA 97:5083–5088

    Article  CAS  Google Scholar 

  22. Slupphaug G, Mol CD, Kavli B, Arvai AS, Krokan HE, Tainer JA (1996) Nature 384:87–92

    Article  CAS  Google Scholar 

  23. Lanes O, Leiros I, Smalås AO, Willassen NP (2002) Extremophiles 6:73–86

    Article  CAS  Google Scholar 

  24. Dinner AR, Blackburn GM, Karplus M (2001) Nature 413:752–755

    Article  CAS  Google Scholar 

  25. Pearlman DA, Case DA, Caldwell JW, Ross WS, Cheatham TE, Debolt S, Ferguson D, Seibel G, Kollman P (1995) Comput Phys Commun 91:1–41

    Article  CAS  Google Scholar 

  26. Wang JM, Cieplak P, Kollman PA (2000) J Comput Chem 21:1049–1074

    Article  CAS  Google Scholar 

  27. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) J Chem Phys 79:926–935

    Article  CAS  Google Scholar 

  28. Berendsen HJC, Postma JPM, Vangunsteren WF, Dinola A, Haak JR (1984) J Chem Phys 81:3684–3690

    Article  CAS  Google Scholar 

  29. Darden T, York D, Pedersen L (1993) J Chem Phys 98:10089–10092

    Article  CAS  Google Scholar 

  30. Ryckaert JP, Ciccotti G, Berendsen HJC (1977) J Comput Phys 23:327–341

    Article  CAS  Google Scholar 

  31. Kollman PA, Massova I, Reyes C, Kuhn B, Huo SH, Chong L, Lee M, Lee T, Duan Y, Wang W, Donini O, Cieplak P, Srinivasan J, Case DA, Cheatham TE (2000) Acc Chem Res 33:889–897

    Article  CAS  Google Scholar 

  32. Massova I, Kollman PA (1999) J Am Chem Soc 121:8133–8143

    Article  CAS  Google Scholar 

  33. Srinivasan J, Cheatham TE, Cieplak P, Kollman PA, Case DA (1998) J Am Chem Soc 120:9401–9409

    Article  CAS  Google Scholar 

  34. Luo R, David L, Gilson MK (2002) J Comput Chem 23:1244–1253

    Article  CAS  Google Scholar 

  35. Onufriev A, Bashford D, Case DA (2000) J Phys Chem B 104:3712–3720

    Article  CAS  Google Scholar 

  36. Onufriev A, Bashford D, Case DA (2004) Proteins 55:383–394

    Article  CAS  Google Scholar 

  37. Peter C, Oostenbrink C, van Dorp A, van Gunsteren WF (2004) J Chem Phys 120:2652–2661

    Article  CAS  Google Scholar 

  38. Case DA (1994) Curr Opin Struc Biol 4:285–290

    Article  CAS  Google Scholar 

  39. Karplus M, Kushick JN (1981) Macromolecules 14:325–332

    Article  CAS  Google Scholar 

  40. Schafer H, Daura X, Mark AE, van Gunsteren WF (2001) Proteins 43:45–56

    Article  CAS  Google Scholar 

  41. Schafer H, Mark AE, van Gunsteren WF (2000) J Chem Phys 113:7809–7817

    Article  CAS  Google Scholar 

  42. Kuhn B, Kollman PA (2000) J Med Chem 43:3786–3791

    Article  CAS  Google Scholar 

  43. Jayaram B, Sprous D, Beveridge DL (1998) J Phys Chem B 102:9571–9576

    Article  CAS  Google Scholar 

  44. Connolly ML (1983) J Appl Cryst 16:548–558

    Article  CAS  Google Scholar 

  45. Weiser J, Shenkin PS, Still WC (1999) J Comput Chem 20:217–230

    Article  CAS  Google Scholar 

  46. Rocchia W, Alexov E, Honig B (2001) J Phys Chem B 105:6507–6514

    Article  CAS  Google Scholar 

  47. Rocchia W, Sridharan S, Nicholls A, Alexov E, Chiabrera A, Honig B (2002) J Comput Chem 23:128–137

    Article  CAS  Google Scholar 

  48. Moreira IS, Fernandes PA, Ramos MJ (2005) J Mol Struc Theochem 729:11–18

    Article  CAS  Google Scholar 

  49. Jiang YL, Ichikawa Y, Song F, Stivers JT (2003) Biochemistry 42:1922–1929

    Article  CAS  Google Scholar 

  50. Fersht A (1999) Structure and mechanism in protein science. In: Hadler GL (ed) W.H. Freeman and Company, NY

  51. Brigo A, Lee KW, Fogolari F, Mustata GL, Briggs JM (2005) Proteins 59:723–741

    Article  CAS  Google Scholar 

  52. Kuhn B, Kollman PA (2000) J Am Chem Soc 122:3909–3916

    Article  CAS  Google Scholar 

  53. Adekoya OA, Willassen NP, Sylte I (2005) J Biomol Struct Dyn 22:521–531

    CAS  Google Scholar 

  54. Luo C, Xu LF, Zheng SX, Luo Z, Jiang XM, Shen JH, Jiang HL, Liu XF, Zhou MD (2005) Proteins 59:742–756

    Article  CAS  Google Scholar 

  55. Wang W, Kollman PA (2000) J Mol Biol 303:567–582

    Article  CAS  Google Scholar 

  56. Reyes CM, Kollman PA (2000) J Mol Biol 297:1145–1158

    Article  CAS  Google Scholar 

  57. Zhang Q, Schlick T (2006) Biophys J 90:1865–1877

    Article  CAS  Google Scholar 

  58. Gohlke H, Case DA (2004) J Comput Chem 25:238–250

    Article  CAS  Google Scholar 

  59. Cao CY, Jiang YL, Stivers JT, Song FH (2004) Nat Struct Mol Biol 11:1230–1236

    Article  CAS  Google Scholar 

  60. Parker CN, Halford SE (1991) Cell 66:781–791

    Article  CAS  Google Scholar 

  61. Pearl LH (2000) Mut Res 460:165–181

    CAS  Google Scholar 

  62. Krosky DJ, Song FH, Stivers JT (2005) Biochemistry 44:5949–5959

    Article  CAS  Google Scholar 

  63. Cao CY, Jiang YL, Krosky DJ, Stivers JT (2006) J Am Chem Soc 128:13034–13035

    Article  CAS  Google Scholar 

  64. Jiang YL, Drohat AC, Ichikawa Y, Stivers JT (2002) J Biol Chem 277:15385–15392

    Article  CAS  Google Scholar 

  65. Mol CD, Arvai AS, Sanderson RJ, Slupphaug G, Kavli B, Krokan HE, Mosbaugh DW, Tainer JA (1995) Cell 82:701–708

    Article  CAS  Google Scholar 

  66. Wong I, Lundquist AJ, Bernards AS, Mosbaugh DW (2002) J Biol Chem 277:19424–19432

    Article  CAS  Google Scholar 

  67. Chen CY, Mosbaugh DW, Bennett SE (2005) DNA Repair 4:793–805

    Article  CAS  Google Scholar 

  68. Jiang YL, Kwon K, Stivers JT (2001) J Biol Chem 276:42347–42354

    Article  CAS  Google Scholar 

  69. Stivers JT, Pankiewicz KW, Watanabe KA (1999) Biochemistry 38:952–963

    Article  CAS  Google Scholar 

  70. DeLano WL (2002) The pyMol molecular graphics system. DeLano Scientific, San Carlos, CA, USA

    Google Scholar 

Download references

Acknowledgements

Finacial support from the Research Council of Norway is gratefully acknowledged. The Norwegian Structural Biology Centre is supported by the Functional Genomics Program (FUGE) of the Research Council of Norway.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Bjørn O. Brandsdal.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Olufsen, M., Smalås, A.O. & Brandsdal, B.O. Electrostatic interactions play an essential role in DNA repair and cold-adaptation of Uracil DNA glycosylase. J Mol Model 14, 201–213 (2008). https://doi.org/10.1007/s00894-007-0261-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00894-007-0261-0

Keywords

Navigation