Journal of Chemical Sciences

, Volume 127, Issue 10, pp 1701–1713 | Cite as

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

  • U DEVA PRIYAKUMAREmail author


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.

Graphical Abstract

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.


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



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.

Supplementary material

12039_2015_942_MOESM1_ESM.docx (1.8 mb)
(DOCX 1.82 MB)


  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 11535CrossRefGoogle Scholar
  2. 2.
    Nowotny M, Gaidamakov S A, Crouch R J and Yang W 2005 Cell 121 1005CrossRefGoogle Scholar
  3. 3.
    Qiu J, Qian Y, Frank P, Wintersberger U and Shen B 1999 Mol. Cell. Biol. 19 8361CrossRefGoogle Scholar
  4. 4.
    Crouch R J and Toulme J J 1998 In Ribonucleases H (INSERM Editions: Paris)Google Scholar
  5. 5.
    Tadokoro T and Kanaya S 2009 FEBS J. 276 1482CrossRefGoogle Scholar
  6. 6.
    Worrall J A R and Luisi B F 2007 Curr. Opin. Struct. Biol. 17 128CrossRefGoogle Scholar
  7. 7.
    Cerritelli S M and Crouch R J 2009 FEBS J. 276 1494CrossRefGoogle Scholar
  8. 8.
    Katayanagi K, Miyagawa M, Matsushima M, Ishikawa M, Kanaya S, Ikehara M, Matsuzaki T and Morikawa K 1990 Nature 347 306CrossRefGoogle 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 1029CrossRefGoogle Scholar
  10. 10.
    Yang W, Hendrickson W A, Crouch R J and Satow Y 1990 Science 249 1398CrossRefGoogle 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 4615Google 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 623CrossRefGoogle Scholar
  13. 13.
    Kanaya S and Crouch R J 1983 J. Biol. Chem. 258 1276Google Scholar
  14. 14.
    Oda Y, Iwai S, Ohtsuka E, Ishikawa M, Ikehara M and Nakamura H 1993 Nucleic Acid Res. 21 4690CrossRefGoogle Scholar
  15. 15.
    Lai L, Yokota H, Hung L W, Kim R and Kim S H 2000 Struct. Fold. Des. 8 897CrossRefGoogle Scholar
  16. 16.
    Ariyoshi M, Vassylyev D G, Iwasaki H, Nakamura H, Shinaweregawa H and Morikawa K 1994 Cell 78 1063CrossRefGoogle 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 6601CrossRefGoogle Scholar
  18. 18.
    Rice P A and Baker T A 2001 Nat. Struct. Biol. 8 302CrossRefGoogle Scholar
  19. 19.
    Yang W and Steitz T A 1995 Structure 3 131CrossRefGoogle Scholar
  20. 20.
    Gyi J I, Lane A N, Conn G L and Brown T 1998 Biochemistry 37 73CrossRefGoogle Scholar
  21. 21.
    Suresh G and Priyakumar U D 2014 Phys. Chem. Chem. Phys. 16 18148CrossRefGoogle Scholar
  22. 22.
    Nowotny M, Gaidamakov S A, Ghirlando R, Cerritelli S M, Crouch R J and Yang W 2007 Mol. Cell 28 264CrossRefGoogle Scholar
  23. 23.
    Steitz T A and Steitz J A 1993 Proc. Natl. Acad. Sci. USA 90 6498CrossRefGoogle Scholar
  24. 24.
    De Vivo M, Dal Peraro M and Klein M L 2008 J. Am. Chem. Soc. 130 10955CrossRefGoogle Scholar
  25. 25.
    Krakowiak A, Owczarek A, Koziolkiewicz M and Stec W J 2002 Chembiochem 3 1242CrossRefGoogle Scholar
  26. 26.
    Cassano A G, Anderson V E and Harris M E 2004 Biopolymers 73 110CrossRefGoogle Scholar
  27. 27.
    Haruki M, Noguchi E, Kanaya S and Crouch R J 1997 J. Biol. Chem. 272 22015CrossRefGoogle Scholar
  28. 28.
    Cerritelli S M, Frolova E G, Feng C, Grinberg A, Love P E and Crouch R J 2003 Mol. Cell 11 807CrossRefGoogle Scholar
  29. 29.
    Luisi B F, Xu W X, Otwinowski Z, Freedman L P, Yamamoto K R and Sigler P B 1991 Nature 352 497CrossRefGoogle Scholar
  30. 30.
    Nelson D L and Cox M M 2005 In Lehninger’s Principles of Biochemistry 4th ed. (New York: W H Freeman)Google Scholar
  31. 31.
    Draper D E 1993 Proc. Natl. Acad. Sci. USA 90 7429CrossRefGoogle Scholar
  32. 32.
    Duan Y, Wilkosz P and Rosenberg J M 1996 J. Mol. Biol. 264 546CrossRefGoogle 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 5368CrossRefGoogle 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 1545CrossRefGoogle Scholar
  35. 35.
    Yang X, Gérczei T, Glover L and Correll C C 2001 Nature Struct. Biol. 8 968CrossRefGoogle Scholar
  36. 36.
    Sen S and Nilsson L 1999 Biophys. J. 77 1782CrossRefGoogle Scholar
  37. 37.
    Reyes C M, Nifosı R, Frankel A D and Kollman P A 2001 Biophys. J. 80 2833CrossRefGoogle 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 12415CrossRefGoogle 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 196CrossRefGoogle Scholar
  40. 40.
    Furini S, Barbini P and Domene C 2013 Nucleic Acids Res. 41 3963CrossRefGoogle Scholar
  41. 41.
    Priyakumar U D, Harika G and Suresh G 2010 J. Phys. Chem. B 114 16548CrossRefGoogle Scholar
  42. 42.
    Rosta E, Nowotny M, Yang W and Hummer G 2011 J. Am. Chem. Soc. 133 8934CrossRefGoogle Scholar
  43. 43.
    Maláč K and Barvík I 2013 J. Mol. Graph. Model. 44 81CrossRefGoogle 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 1545CrossRefGoogle Scholar
  45. 45.
    Priyakumar U D, Ramakrishna S, Nagarjuna K R and Reddy S K 2010 J. Phys. Chem. B 114 1707CrossRefGoogle Scholar
  46. 46.
    Suresh G and Priyakumar U D 2014 J. Phys. Chem. B 118 5853CrossRefGoogle Scholar
  47. 47.
    Jorgensen W L, Chandrasekhar J, Madura J D, Impey R W and Klein M L 1983 J. Chem. Phys. 79 926CrossRefGoogle Scholar
  48. 48.
    Ryckaert J P, Ciccotti G and Berendsen H J C 1977 J. Comput. Phys. 23 327CrossRefGoogle Scholar
  49. 49.
    Field M J and Karplus M 1992 In CRYSTAL: Program for Crystal Calculations in CHARMM (Harvard University: Cambridge, MA)Google Scholar
  50. 50.
    Darden T, Perera L, Li L P and Pedersen L 1999 Structure 7 R55CrossRefGoogle Scholar
  51. 51.
    Essmann U, Perera L, Berkowitz M L, Darden T A, Lee H and Pedersen L G 1995 J. Chem. Phys. 103 8577CrossRefGoogle Scholar
  52. 52.
    Steinbach P J and Brooks B R 1994 J. Comput. Chem. 15 667CrossRefGoogle 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 1781CrossRefGoogle Scholar
  54. 54.
    Foloppe N and MacKerell A D 2000 J. Comput. Chem. 21 86CrossRefGoogle Scholar
  55. 55.
    MacKerell A D and Banavali N K 2000 J. Comput. Chem. 21 105CrossRefGoogle 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 3586CrossRefGoogle Scholar
  57. 57.
    MacKerell A D, Feig M and Brooks C L 2004 J. Comput. Chem. 25 1400CrossRefGoogle Scholar
  58. 58.
    Suresh G and Priyakumar U D 2013 J. Phys. Chem. B 117 5556CrossRefGoogle Scholar
  59. 59.
    Feller S E, Zhang Y, Pastor R W and Brooks R W 1995 J. Chem. Phys. 103 4613CrossRefGoogle Scholar
  60. 60.
    Hoover W G 1985 Phy. Rev. A 31 1695CrossRefGoogle Scholar
  61. 61.
    Priyakumar U D and MacKerell A D 2010 J. Mol. Biol. 396 1422CrossRefGoogle Scholar
  62. 62.
    Humphrey W, Dalke A and Schulten K 1996 J. Molec. Graphics 14 33CrossRefGoogle Scholar
  63. 63.
    Lavery R, Moakher M, Maddocks J H, Petkeviciute D and Zakrzewska K 2009 Nucleic Acids Res. 37 5917CrossRefGoogle Scholar
  64. 64.
    Stafford K A and Palmer A G 2014 F1000 Research 3 67Google Scholar
  65. 65.
    Rychlik M P, Chon H, Cerritelli S M, Klimek P, Crouch R J and Nowotny M 2010 Molecular Cell 40 658CrossRefGoogle Scholar
  66. 66.
    Babu C S, Dudev T and Lim C 2013 J. Am. Chem. Soc. 135 6541CrossRefGoogle Scholar

Copyright information

© Indian Academy of Sciences 2015

Authors and Affiliations

  1. 1.Center for Computational Natural Sciences and BioinformaticsInternational Institute of Information TechnologyHyderabadIndia

Personalised recommendations