Atomistic details of the molecular recognition of DNA-RNA hybrid duplex by ribonuclease H enzyme

Abstract

Bacillus halodurans (Bh) ribonuclease H (RNase H) belongs to the nucleotidyl-transferase (NT) superfamily and is a prototypical member of a large family of enzymes that use two-metal ion (Mg2+ or Mn2+) catalysis to cleave nucleic acids. Long timescale molecular dynamics simulations have been performed on the BhRNase H-DNA-RNA hybrid complex and the respective monomers to understand the recognition mechanism, conformational preorganization, active site dynamics and energetics involved in the complex formation. Several structural and energetic analyses were performed and significant structural changes are observed in enzyme and hybrid duplex during complex formation. Hybrid molecule binding to RNase H enzyme leads to conformational changes in the DNA strand. The ability of the DNA strand in the hybrid duplex to sample conformations corresponding to typical A- and B-type nucleic acids and the characteristic minor groove widthseem to be crucial for efficient binding. Sugar moieties in certain positions interacting with the protein structure undergo notable conformational transitions. The water coordination and arrangement around the metal ions in active site region are quite stable, suggesting their important role in enzymatic catalysis. Details of key interactions found at the interface of enzyme-nucleic acid complex that are responsible for its stability are discussed.

Molecular dynamics simulation results have shown that the DNA nucleotides of DNA-RNA hybrid that are interacting with ribonuclease H enzyme show interesting conformational changes upon binding.

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

Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7
Figure 8

References

  1. 1.

    Nakamura H, Oda Y, Iwai S, Inoue H, Ohtsuka E, Kanaya S, Kimura S, Katsuda C, Katayanagi K and Morikawa K 1991 Proc. Natl. Acad. Sci. USA 88 11535

    Article  CAS  Google Scholar 

  2. 2.

    Nowotny M, Gaidamakov S A, Crouch R J and Yang W 2005 Cell 121 1005

    Article  CAS  Google Scholar 

  3. 3.

    Qiu J, Qian Y, Frank P, Wintersberger U and Shen B 1999 Mol. Cell. Biol. 19 8361

    Article  CAS  Google Scholar 

  4. 4.

    Crouch R J and Toulme J J 1998 In Ribonucleases H (INSERM Editions: Paris)

  5. 5.

    Tadokoro T and Kanaya S 2009 FEBS J. 276 1482

    Article  CAS  Google Scholar 

  6. 6.

    Worrall J A R and Luisi B F 2007 Curr. Opin. Struct. Biol. 17 128

    Article  CAS  Google Scholar 

  7. 7.

    Cerritelli S M and Crouch R J 2009 FEBS J. 276 1494

    Article  CAS  Google Scholar 

  8. 8.

    Katayanagi K, Miyagawa M, Matsushima M, Ishikawa M, Kanaya S, Ikehara M, Matsuzaki T and Morikawa K 1990 Nature 347 306

    Article  CAS  Google Scholar 

  9. 9.

    Katayanagi K, Miyagawa M, Matsushima M, Ishikawa M, Kanaya S, Nakamura H, Ikehara M, Matsuzaki T and Morikawa K 1992 J. Mol. Biol. 223 1029

    Article  CAS  Google Scholar 

  10. 10.

    Yang W, Hendrickson W A, Crouch R J and Satow Y 1990 Science 249 1398

    Article  CAS  Google Scholar 

  11. 11.

    Kanaya S, Kohara A, Miura Y, Sekiguchi A, Iwai S, Inoue H, Ohtsuka E and Ikehara M 1990 J. Biol. Chem. 265 4615

    CAS  Google Scholar 

  12. 12.

    Haruki M, Noguchi E, Nakai C, Liu Y Y, Oobatake M, Itaya M and Kanaya S 1994 Eur. J. Bio. Chem. 220 623

    Article  CAS  Google Scholar 

  13. 13.

    Kanaya S and Crouch R J 1983 J. Biol. Chem. 258 1276

    CAS  Google Scholar 

  14. 14.

    Oda Y, Iwai S, Ohtsuka E, Ishikawa M, Ikehara M and Nakamura H 1993 Nucleic Acid Res. 21 4690

    Article  CAS  Google Scholar 

  15. 15.

    Lai L, Yokota H, Hung L W, Kim R and Kim S H 2000 Struct. Fold. Des. 8 897

    Article  CAS  Google Scholar 

  16. 16.

    Ariyoshi M, Vassylyev D G, Iwasaki H, Nakamura H, Shinaweregawa H and Morikawa K 1994 Cell 78 1063

    Article  CAS  Google Scholar 

  17. 17.

    Ceschini S, Keeley A, McAlister M S, Oram M, Phelan J, Pearl L H, Tsaneva I R and Barrett T E 2001 EMBO J. 20 6601

    Article  CAS  Google Scholar 

  18. 18.

    Rice P A and Baker T A 2001 Nat. Struct. Biol. 8 302

    Article  CAS  Google Scholar 

  19. 19.

    Yang W and Steitz T A 1995 Structure 3 131

    Article  CAS  Google Scholar 

  20. 20.

    Gyi J I, Lane A N, Conn G L and Brown T 1998 Biochemistry 37 73

    Article  CAS  Google Scholar 

  21. 21.

    Suresh G and Priyakumar U D 2014 Phys. Chem. Chem. Phys. 16 18148

    Article  CAS  Google Scholar 

  22. 22.

    Nowotny M, Gaidamakov S A, Ghirlando R, Cerritelli S M, Crouch R J and Yang W 2007 Mol. Cell 28 264

    Article  CAS  Google Scholar 

  23. 23.

    Steitz T A and Steitz J A 1993 Proc. Natl. Acad. Sci. USA 90 6498

    Article  CAS  Google Scholar 

  24. 24.

    De Vivo M, Dal Peraro M and Klein M L 2008 J. Am. Chem. Soc. 130 10955

    Article  CAS  Google Scholar 

  25. 25.

    Krakowiak A, Owczarek A, Koziolkiewicz M and Stec W J 2002 Chembiochem 3 1242

    Article  CAS  Google Scholar 

  26. 26.

    Cassano A G, Anderson V E and Harris M E 2004 Biopolymers 73 110

    Article  CAS  Google Scholar 

  27. 27.

    Haruki M, Noguchi E, Kanaya S and Crouch R J 1997 J. Biol. Chem. 272 22015

    Article  CAS  Google Scholar 

  28. 28.

    Cerritelli S M, Frolova E G, Feng C, Grinberg A, Love P E and Crouch R J 2003 Mol. Cell 11 807

    Article  CAS  Google Scholar 

  29. 29.

    Luisi B F, Xu W X, Otwinowski Z, Freedman L P, Yamamoto K R and Sigler P B 1991 Nature 352 497

    Article  CAS  Google Scholar 

  30. 30.

    Nelson D L and Cox M M 2005 In Lehninger’s Principles of Biochemistry 4th ed. (New York: W H Freeman)

  31. 31.

    Draper D E 1993 Proc. Natl. Acad. Sci. USA 90 7429

    Article  CAS  Google Scholar 

  32. 32.

    Duan Y, Wilkosz P and Rosenberg J M 1996 J. Mol. Biol. 264 546

    Article  CAS  Google Scholar 

  33. 33.

    Arndt J W, Gong W, Zhong X, Showalter A K, Liu J, Dunlap C A, Lin Z, Paxson C, Tsai M D and Chan M K 2001 Biochemistry 40 5368

    Article  CAS  Google Scholar 

  34. 34.

    Tishchenko S, Nikonova E, Nikulin A, Nevskaya N, Volchkov S, Piendl W, Garber M and Nikonov S 2006 Acta Cryst. D 62 1545

    Article  CAS  Google Scholar 

  35. 35.

    Yang X, Gérczei T, Glover L and Correll C C 2001 Nature Struct. Biol. 8 968

    Article  CAS  Google Scholar 

  36. 36.

    Sen S and Nilsson L 1999 Biophys. J. 77 1782

    Article  CAS  Google Scholar 

  37. 37.

    Reyes C M, Nifosı R, Frankel A D and Kollman P A 2001 Biophys. J. 80 2833

    Article  CAS  Google Scholar 

  38. 38.

    Chen L, Zhang J, Yu L, Zheng Q C, Chu W T, Xue Q, Zhang H X and Sun C C 2012 J. Phys. Chem. B 116 12415

    Article  CAS  Google Scholar 

  39. 39.

    Driessen R P, Meng H, Suresh G, Shahapure R, Lanzani G, Priyakumar U D, White M F, Schiessel H, van Noort J and Dame R T 2013 Nucleic Acids Res. 41 196

    Article  CAS  Google Scholar 

  40. 40.

    Furini S, Barbini P and Domene C 2013 Nucleic Acids Res. 41 3963

    Article  CAS  Google Scholar 

  41. 41.

    Priyakumar U D, Harika G and Suresh G 2010 J. Phys. Chem. B 114 16548

    Article  CAS  Google Scholar 

  42. 42.

    Rosta E, Nowotny M, Yang W and Hummer G 2011 J. Am. Chem. Soc. 133 8934

    Article  CAS  Google Scholar 

  43. 43.

    Maláč K and Barvík I 2013 J. Mol. Graph. Model. 44 81

    Article  Google Scholar 

  44. 44.

    Brooks B R, Brooks C L, MacKerell A D, Nilsson L, Petrella R J, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner A R, Feig M, Fischer S, Gao J, Hodoscek M, Im W, Kuczera K, Lazaridis T, Ma J, Ovchinnikov V, Paci E, Pastor R W, Post C B, Pu J Z, Schaefer M, Tidor B, Venable R M, Woodcock H L, Wu X, Yang W, York D M and Karplus M 2009 J. Comput. Chem. 30 1545

    Article  CAS  Google Scholar 

  45. 45.

    Priyakumar U D, Ramakrishna S, Nagarjuna K R and Reddy S K 2010 J. Phys. Chem. B 114 1707

    Article  CAS  Google Scholar 

  46. 46.

    Suresh G and Priyakumar U D 2014 J. Phys. Chem. B 118 5853

    Article  CAS  Google Scholar 

  47. 47.

    Jorgensen W L, Chandrasekhar J, Madura J D, Impey R W and Klein M L 1983 J. Chem. Phys. 79 926

    Article  CAS  Google Scholar 

  48. 48.

    Ryckaert J P, Ciccotti G and Berendsen H J C 1977 J. Comput. Phys. 23 327

    Article  CAS  Google Scholar 

  49. 49.

    Field M J and Karplus M 1992 In CRYSTAL: Program for Crystal Calculations in CHARMM (Harvard University: Cambridge, MA)

  50. 50.

    Darden T, Perera L, Li L P and Pedersen L 1999 Structure 7 R55

    Article  CAS  Google Scholar 

  51. 51.

    Essmann U, Perera L, Berkowitz M L, Darden T A, Lee H and Pedersen L G 1995 J. Chem. Phys. 103 8577

    Article  CAS  Google Scholar 

  52. 52.

    Steinbach P J and Brooks B R 1994 J. Comput. Chem. 15 667

    Article  CAS  Google Scholar 

  53. 53.

    Phillips J C, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel R D, Kale L and Schulten K 2005 J. Comput. Chem. 26 1781

    Article  CAS  Google Scholar 

  54. 54.

    Foloppe N and MacKerell A D 2000 J. Comput. Chem. 21 86

    Article  CAS  Google Scholar 

  55. 55.

    MacKerell A D and Banavali N K 2000 J. Comput. Chem. 21 105

    Article  CAS  Google Scholar 

  56. 56.

    MacKerell A D, Bashford D, Bellott D R L, Evanseck J D, Field M J, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau F T K, Mattos C, Michnick S, Ngo T, Nguyen D T, Prodhom B, Reiher W E, Roux B, Schlenkrich M, Smith J C, Stote R, Straub J, Watanabe M, Wiorkiewicz-Kuczera J, Yin D and Karplus M 1998 J. Phys. Chem. B 102 3586

    Article  CAS  Google Scholar 

  57. 57.

    MacKerell A D, Feig M and Brooks C L 2004 J. Comput. Chem. 25 1400

    Article  CAS  Google Scholar 

  58. 58.

    Suresh G and Priyakumar U D 2013 J. Phys. Chem. B 117 5556

    Article  CAS  Google Scholar 

  59. 59.

    Feller S E, Zhang Y, Pastor R W and Brooks R W 1995 J. Chem. Phys. 103 4613

    Article  CAS  Google Scholar 

  60. 60.

    Hoover W G 1985 Phy. Rev. A 31 1695

    Article  Google Scholar 

  61. 61.

    Priyakumar U D and MacKerell A D 2010 J. Mol. Biol. 396 1422

    Article  CAS  Google Scholar 

  62. 62.

    Humphrey W, Dalke A and Schulten K 1996 J. Molec. Graphics 14 33

    Article  CAS  Google Scholar 

  63. 63.

    Lavery R, Moakher M, Maddocks J H, Petkeviciute D and Zakrzewska K 2009 Nucleic Acids Res. 37 5917

    Article  CAS  Google Scholar 

  64. 64.

    Stafford K A and Palmer A G 2014 F1000 Research 3 67

    Google Scholar 

  65. 65.

    Rychlik M P, Chon H, Cerritelli S M, Klimek P, Crouch R J and Nowotny M 2010 Molecular Cell 40 658

    Article  CAS  Google Scholar 

  66. 66.

    Babu C S, Dudev T and Lim C 2013 J. Am. Chem. Soc. 135 6541

    Article  Google Scholar 

Download references

Acknowledgements

We thank AICTE, and Department of Atomic Energy-BRNS (37(2)/14/05/2015/BRNS/20046) for financial assistance. GS thanks Council of Scientific and Industrial Research (CSIR), India for senior research fellowship.

Author information

Affiliations

Authors

Corresponding author

Correspondence to U DEVA PRIYAKUMAR.

Additional information

Supplementary Information

This includes methods to calculate hydration numbers and hydrogen bonds (Supplementary methods), RMSD and radius of gyration (figure S1; table S1), Ramachandran plot (figure S2), hydrogen bond distances (figure S3), helical parameters (figures S4–S5), backbone angles (figure S6), buried surface area (figure S7), hydrogen bond distances (figure S8), pseudorotation angles (table S2), stacking interactions (table S3), hydration numbers and sasa (table S4), and statistics of hydrogen bonds (tables S5, S6, S7). Supplementary Information is available at www.ias.ac.in/chemsci.

Electronic supplementary material

Below is the link to the electronic supplementary material.

(DOCX 1.82 MB)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

SURESH, G., PRIYAKUMAR, U.D. Atomistic details of the molecular recognition of DNA-RNA hybrid duplex by ribonuclease H enzyme. J Chem Sci 127, 1701–1713 (2015). https://doi.org/10.1007/s12039-015-0942-7

Download citation

Keywords

  • HIV-1 reverse transcriptase
  • MD simulations
  • ribonuclease H activity
  • retroviral therapy
  • conformational transition
  • protein-nucleic acid interactions.