Journal of Molecular Modeling

, Volume 14, Issue 3, pp 201–213 | Cite as

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

  • Magne Olufsen
  • Arne O. Smalås
  • Bjørn O. Brandsdal
Original Paper

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.

Figure

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

Keywords

Continuum electrostatics Free energy calculations Molecular simulations Protein-DNA binding Uracil DNA glycosylase 

References

  1. 1.
    Hochachka PW, Somero GN (1984) Temperature adaptation, in Biochemical adaptations. Princeton University Press, Princeton, NJ, pp 355–449Google Scholar
  2. 2.
    Fields PA, Somero GN (1998) Proc Natl Acad Sci USA 95:11476–11481CrossRefGoogle Scholar
  3. 3.
    Georlette D, Damien B, Blaise V, Depiereux E, Uversky VN, Gerday C, Feller G (2003) J Biol Chem 278:37015–37023CrossRefGoogle Scholar
  4. 4.
    Leiros I, Moe E, Lanes O, Smalås AO, Willassen NP (2003) Acta Crystallogr D Biol Crystallogr 59:1357–1365CrossRefGoogle Scholar
  5. 5.
    Olufsen M, Smalås AO, Moe E, Brandsdal BO (2005) J Biol Chem 280:18042–18048CrossRefGoogle Scholar
  6. 6.
    Smalås AO, Heimstad ES, Hordvik A, Willassen NP, Male R (1994) Proteins 20:149–166CrossRefGoogle Scholar
  7. 7.
    Brandsdal BO, Heimstad ES, Sylte I, Smalås AO (1999) J Biomol Struct Dyn 17:493–506Google Scholar
  8. 8.
    Russell RJM, Gerike U, Danson MJ, Hough DW, Taylor GL (1998) Structure 6:351–361CrossRefGoogle Scholar
  9. 9.
    Kumar S, Nussinov R (2004) ChemBioChem 5:280–290CrossRefGoogle Scholar
  10. 10.
    Gorfe AA, Brandsdal BO, Leiros HKS, Helland R, Smalås AO (2000) Proteins 40:207–217CrossRefGoogle Scholar
  11. 11.
    Brandsdal BO, Smalås AO, Åqvist J (2001) FEBS Lett 499:171–175CrossRefGoogle Scholar
  12. 12.
    Moe E, Leiros I, Riise EK, Olufsen M, Lanes O, Smalås A, Willassen NP (2004) J Mol Biol 343:1221–1230CrossRefGoogle Scholar
  13. 13.
    Lindahl T, Nyberg B (1974) Biochemistry 13:3405–3410CrossRefGoogle Scholar
  14. 14.
    Krokan HE, Standal R, Slupphaug G (1997) Biochem J 325:1–16Google Scholar
  15. 15.
    Mol CD, Arvai AS, Slupphaug G, Kavli B, Alseth I, Krokan HE, Tainer JA (1995) Cell 80:869–878CrossRefGoogle Scholar
  16. 16.
    Savva R, Mcauleyhecht K, Brown T, Pearl L (1995) Nature 373:487–493CrossRefGoogle Scholar
  17. 17.
    Ravishankar R, Sagar MB, Roy S, Purnapatre K, Handa P, Varshney U, Vijayan M (1998) Nucleic Acids Res 26:4880–4887CrossRefGoogle Scholar
  18. 18.
    Geoui T, Buisson M, Tarbouriech N, Burmeister WP (2007) J Mol Biol 366:117–131CrossRefGoogle Scholar
  19. 19.
    Bianchet MA, Seiple LA, Jiang YL, Ichikawa Y, Amzel LM, Stivers JT (2003) Biochemistry 42:12455–12460CrossRefGoogle Scholar
  20. 20.
    Parikh SS, Mol CD, Slupphaug G, Bharati S, Krokan HE, Tainer JA (1998) EMBO J 17:5214–5226CrossRefGoogle Scholar
  21. 21.
    Parikh SS, Walcher G, Jones GD, Slupphaug G, Krokan HE, Blackburn GM, Tainer JA (2000) Proc Natl Acad Sci USA 97:5083–5088CrossRefGoogle Scholar
  22. 22.
    Slupphaug G, Mol CD, Kavli B, Arvai AS, Krokan HE, Tainer JA (1996) Nature 384:87–92CrossRefGoogle Scholar
  23. 23.
    Lanes O, Leiros I, Smalås AO, Willassen NP (2002) Extremophiles 6:73–86CrossRefGoogle Scholar
  24. 24.
    Dinner AR, Blackburn GM, Karplus M (2001) Nature 413:752–755CrossRefGoogle Scholar
  25. 25.
    Pearlman DA, Case DA, Caldwell JW, Ross WS, Cheatham TE, Debolt S, Ferguson D, Seibel G, Kollman P (1995) Comput Phys Commun 91:1–41CrossRefGoogle Scholar
  26. 26.
    Wang JM, Cieplak P, Kollman PA (2000) J Comput Chem 21:1049–1074CrossRefGoogle Scholar
  27. 27.
    Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) J Chem Phys 79:926–935CrossRefGoogle Scholar
  28. 28.
    Berendsen HJC, Postma JPM, Vangunsteren WF, Dinola A, Haak JR (1984) J Chem Phys 81:3684–3690CrossRefGoogle Scholar
  29. 29.
    Darden T, York D, Pedersen L (1993) J Chem Phys 98:10089–10092CrossRefGoogle Scholar
  30. 30.
    Ryckaert JP, Ciccotti G, Berendsen HJC (1977) J Comput Phys 23:327–341CrossRefGoogle Scholar
  31. 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 33:889–897CrossRefGoogle Scholar
  32. 32.
    Massova I, Kollman PA (1999) J Am Chem Soc 121:8133–8143CrossRefGoogle Scholar
  33. 33.
    Srinivasan J, Cheatham TE, Cieplak P, Kollman PA, Case DA (1998) J Am Chem Soc 120:9401–9409CrossRefGoogle Scholar
  34. 34.
    Luo R, David L, Gilson MK (2002) J Comput Chem 23:1244–1253CrossRefGoogle Scholar
  35. 35.
    Onufriev A, Bashford D, Case DA (2000) J Phys Chem B 104:3712–3720CrossRefGoogle Scholar
  36. 36.
    Onufriev A, Bashford D, Case DA (2004) Proteins 55:383–394CrossRefGoogle Scholar
  37. 37.
    Peter C, Oostenbrink C, van Dorp A, van Gunsteren WF (2004) J Chem Phys 120:2652–2661CrossRefGoogle Scholar
  38. 38.
    Case DA (1994) Curr Opin Struc Biol 4:285–290CrossRefGoogle Scholar
  39. 39.
    Karplus M, Kushick JN (1981) Macromolecules 14:325–332CrossRefGoogle Scholar
  40. 40.
    Schafer H, Daura X, Mark AE, van Gunsteren WF (2001) Proteins 43:45–56CrossRefGoogle Scholar
  41. 41.
    Schafer H, Mark AE, van Gunsteren WF (2000) J Chem Phys 113:7809–7817CrossRefGoogle Scholar
  42. 42.
    Kuhn B, Kollman PA (2000) J Med Chem 43:3786–3791CrossRefGoogle Scholar
  43. 43.
    Jayaram B, Sprous D, Beveridge DL (1998) J Phys Chem B 102:9571–9576CrossRefGoogle Scholar
  44. 44.
    Connolly ML (1983) J Appl Cryst 16:548–558CrossRefGoogle Scholar
  45. 45.
    Weiser J, Shenkin PS, Still WC (1999) J Comput Chem 20:217–230CrossRefGoogle Scholar
  46. 46.
    Rocchia W, Alexov E, Honig B (2001) J Phys Chem B 105:6507–6514CrossRefGoogle Scholar
  47. 47.
    Rocchia W, Sridharan S, Nicholls A, Alexov E, Chiabrera A, Honig B (2002) J Comput Chem 23:128–137CrossRefGoogle Scholar
  48. 48.
    Moreira IS, Fernandes PA, Ramos MJ (2005) J Mol Struc Theochem 729:11–18CrossRefGoogle Scholar
  49. 49.
    Jiang YL, Ichikawa Y, Song F, Stivers JT (2003) Biochemistry 42:1922–1929CrossRefGoogle Scholar
  50. 50.
    Fersht A (1999) Structure and mechanism in protein science. In: Hadler GL (ed) W.H. Freeman and Company, NYGoogle Scholar
  51. 51.
    Brigo A, Lee KW, Fogolari F, Mustata GL, Briggs JM (2005) Proteins 59:723–741CrossRefGoogle Scholar
  52. 52.
    Kuhn B, Kollman PA (2000) J Am Chem Soc 122:3909–3916CrossRefGoogle Scholar
  53. 53.
    Adekoya OA, Willassen NP, Sylte I (2005) J Biomol Struct Dyn 22:521–531Google Scholar
  54. 54.
    Luo C, Xu LF, Zheng SX, Luo Z, Jiang XM, Shen JH, Jiang HL, Liu XF, Zhou MD (2005) Proteins 59:742–756CrossRefGoogle Scholar
  55. 55.
    Wang W, Kollman PA (2000) J Mol Biol 303:567–582CrossRefGoogle Scholar
  56. 56.
    Reyes CM, Kollman PA (2000) J Mol Biol 297:1145–1158CrossRefGoogle Scholar
  57. 57.
    Zhang Q, Schlick T (2006) Biophys J 90:1865–1877CrossRefGoogle Scholar
  58. 58.
    Gohlke H, Case DA (2004) J Comput Chem 25:238–250CrossRefGoogle Scholar
  59. 59.
    Cao CY, Jiang YL, Stivers JT, Song FH (2004) Nat Struct Mol Biol 11:1230–1236CrossRefGoogle Scholar
  60. 60.
    Parker CN, Halford SE (1991) Cell 66:781–791CrossRefGoogle Scholar
  61. 61.
    Pearl LH (2000) Mut Res 460:165–181Google Scholar
  62. 62.
    Krosky DJ, Song FH, Stivers JT (2005) Biochemistry 44:5949–5959CrossRefGoogle Scholar
  63. 63.
    Cao CY, Jiang YL, Krosky DJ, Stivers JT (2006) J Am Chem Soc 128:13034–13035CrossRefGoogle Scholar
  64. 64.
    Jiang YL, Drohat AC, Ichikawa Y, Stivers JT (2002) J Biol Chem 277:15385–15392CrossRefGoogle Scholar
  65. 65.
    Mol CD, Arvai AS, Sanderson RJ, Slupphaug G, Kavli B, Krokan HE, Mosbaugh DW, Tainer JA (1995) Cell 82:701–708CrossRefGoogle Scholar
  66. 66.
    Wong I, Lundquist AJ, Bernards AS, Mosbaugh DW (2002) J Biol Chem 277:19424–19432CrossRefGoogle Scholar
  67. 67.
    Chen CY, Mosbaugh DW, Bennett SE (2005) DNA Repair 4:793–805CrossRefGoogle Scholar
  68. 68.
    Jiang YL, Kwon K, Stivers JT (2001) J Biol Chem 276:42347–42354CrossRefGoogle Scholar
  69. 69.
    Stivers JT, Pankiewicz KW, Watanabe KA (1999) Biochemistry 38:952–963CrossRefGoogle Scholar
  70. 70.
    DeLano WL (2002) The pyMol molecular graphics system. DeLano Scientific, San Carlos, CA, USAGoogle Scholar

Copyright information

© Springer-Verlag 2007

Authors and Affiliations

  • Magne Olufsen
    • 1
  • Arne O. Smalås
    • 1
  • Bjørn O. Brandsdal
    • 1
  1. 1.The Norwegian Structural Biology Centre, Department of ChemistryUniversity of TromsøTromsøNorway

Personalised recommendations