Quantum mechanical/molecular mechanical free energy simulations of the self-cleavage reaction in the hepatitis delta virus ribozyme

Journal of the American Chemical Society

Volumn 136, Issue 4, 2014, Pages 1483-1496

  Ganguly, Abir ^a   Thaplyal, Pallavi ^b   Rosta, Edina ^c   Bevilacqua, Philip C ^b   Hammes Schiffer, Sharon ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b PENNSYLVANIA STATE UNIVERSITY   (United States)

^c KING'S COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CATALYTIC METALS; FREE ENERGY SIMULATIONS; HEPATITIS DELTA VIRUS; METAL ION CATALYSIS; NON-BRIDGING OXYGEN; QUANTUM MECHANICAL/MOLECULAR MECHANICAL; SEQUENTIAL MECHANISM; TRANSITION STATE;

CATALYSIS; ENERGY BARRIERS; METAL IONS; MOLECULAR MODELING; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEOPHILES; OXYGEN; PROTON TRANSFER; VIRUSES;

FREE ENERGY;

HEPATITIS DELTA VIRUS RIBOZYME; MAGNESIUM ION; NUCLEOPHILE; OXYGEN; PHOSPHATE; RIBOZYME; SODIUM ION; UNCLASSIFIED DRUG;

ARTICLE; CRYSTAL STRUCTURE; ENERGY; MOLECULAR DYNAMICS; MOLECULAR MECHANICAL FREE ENERGY SIMULATION; NUCLEAR MAGNETIC RESONANCE; PH; PROTON NUCLEAR MAGNETIC RESONANCE; PROTON TRANSPORT; QUANTUM MECHANICAL FREE ENERGY SIMULATION; REACTION ANALYSIS;

HEPATITIS DELTA VIRUS; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; MOLECULAR STRUCTURE; QUANTUM THEORY; RNA, CATALYTIC;

EID: 84893445982     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja4104217     Document Type: Article

References (64)

1. Fedor, M. J.; Williamson, J. R. Nat. Rev. Mol. Cell Biol. 2005, 6, 399-412
2. Golden, B. L.; Hammes-Schiffer, S.; Carey, P. R.; Bevilacqua, P. C. An Integrated Picture of HDV Ribozyme Catalysis. In Biophysics of RNA Folding; Russell, R., Ed.; Springer: New York, 2013; Vol. 3; pp 135-67.
3. Bevilacqua, P. C.; Yajima, R. Curr. Opin. Chem. Biol. 2006, 10, 455-64
4. Lilley, D. M. J. Biochem. Soc. Trans. 2011, 39, 641-46
5. Been, M. D. Curr. Top. Microbiol. Immunol. 2006, 307, 47-65
6. Salehi-Ashtiani, K.; Lupták, A.; Litovchick, A.; Szostak, J. W. Science 2006, 313, 1788-92
7. Webb, C.-H. T.; Riccitelli, N. J.; Ruminski, D. J.; Lupták, A. Science 2009, 326, 953
8. Webb, C.-H. T.; Luptak, A. RNA Biol. 2011, 8, 719-27
9. Perrotta, A. T.; Shih, I.-H.; Been, M. D. Science 1999, 286, 123-26
10. Nakano, S.; Chadalavada, D. M.; Bevilacqua, P. C. Science 2000, 287, 1493-97
11. Gong, B.; Chen, J.-H.; Chase, E.; Chadalavada, D. M.; Yajima, R.; Golden, B. L.; Bevilacqua, P. C.; Carey, P. R. J. Am. Chem. Soc. 2007, 129, 13335-42
12. Guo, M.; Spitale, R. C.; Volpini, R.; Krucinska, J.; Cristalli, G.; Carey, P. R.; Wedekind, J. E. J. Am. Chem. Soc. 2009, 131, 12908-09
13. Gong, B.; Klein, D. J.; Ferre-D'Amare, A. R.; Carey, P. R. J. Am. Chem. Soc. 2011, 133, 14188-91
14. Liberman, J. A.; Guo, M.; Jenkins, J. L.; Krucinska, J.; Chen, Y.; Carey, P. R.; Wedekind, J. E. J. Am. Chem. Soc. 2012, 134, 16933-36
15. Das, S. R.; Piccirilli, J. A. Nat. Chem. Biol. 2005, 1, 45-52
16. Chen, J.-H.; Yajima, R.; Chadalavada, D. M.; Chase, E.; Bevilacqua, P. C.; Golden, B. L. Biochemistry 2010, 49, 6508-18
17. Banáš, P.; Rulíšek, L.; Hánoš ová, V.; Svozil, D.; Walter, N. G.; Šponer, J.; Otyepka, M. J. Phys. Chem. B 2008, 112, 11177-87
18. Lee, T.-S.; Giambasu, G. M.; Harris, M. E.; York, D. M. J. Phys. Chem. Lett. 2011, 2, 2538-43
19. Ganguly, A.; Bevilacqua, P. C.; Hammes-Schiffer, S. J. Phys. Chem. Lett. 2011, 2, 2906-11
20. Veeraraghavan, N.; Ganguly, A.; Golden, B. L.; Bevilacqua, P. C.; Hammes-Schiffer, S. J. Phys. Chem. B 2011, 115, 8346-57
21. Nakano, S.; Proctor, D. J.; Bevilacqua, P. C. Biochemistry 2001, 40, 12022-38
22. Thaplyal, P.; Ganguly, A.; Golden, B. L.; Hammes-Schiffer, S.; Bevilacqua, P. C. Biochemistry 2013, 52, 6499-514
23. DeRose, V. J. Curr. Opin. Struct. Biol. 2003, 13, 317-24
24. Hougland, J. L.; Kravchuk, A. V.; Herschlag, D.; Piccirilli, J. A. PLoS Biol. 2005, 3 e277
25. Chen, J.; Ganguly, A.; Miswan, Z.; Hammes-Schiffer, S.; Bevilacqua, P. C.; Golden, B. L. Biochemistry 2013, 52, 557-67
26. Golden, B. L. Biochemistry 2011, 50, 9424-33
27. Cerrone-Szakal, A. L.; Siegfried, N. A.; Bevilacqua, P. C. J. Am. Chem. Soc. 2008, 130, 14504-20
28. Cui, Q.; Elstner, M.; Kaxiras, E.; Frauenheim, T.; Karplus, M. J. Phys. Chem. B 2001, 105, 569-85
29. Faradjian, A. K.; Elber, R. J. Chem. Phys. 2004, 120, 10880-89
30. Zheng, H.; Zhang, Y. J. Chem. Phys. 2008, 128 204106
31. Pan, A. C.; Sezer, D.; Roux, B. J. Phys. Chem. B 2008, 112, 3432-40
32. Zhu, F.; Hummer, G. Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 19814-19
33. Rosta, E.; Nowotny, M.; Yang, W.; Hummer, G. J. Am. Chem. Soc. 2011, 133, 8934-41
34. Lans, I.; Medina, M.; Rosta, E.; Hummer, G.; Garcia-Viloca, M.; Lluch, J. M.; González-Lafont, À. J. Am. Chem. Soc. 2012, 134, 20544-53
35. Wojtas-Niziurski, W.; Meng, Y.; Roux, B.; Bernèche, S. J. Chem. Theory Comput. 2013, 9, 1885-95
36. Ren, W. Q.; Vanden-Eijnden, E. J. Phys. Chem. B 2005, 109, 6688-93
37. Torrie, G. M.; Valleau, J. P. J. Comput. Phys. 1977, 23, 187-99
38. Veeraraghavan, N.; Ganguly, A.; Chen, J.-H.; Bevilacqua, P. C.; Hammes-Schiffer, S.; Golden, B. L. Biochemistry 2011, 50, 2672-82
39. Veeraraghavan, N.; Bevilacqua, P. C.; Hammes-Schiffer, S. J. Mol. Biol. 2010, 402, 278-91
40. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926-35
41. Desmond; D. E. Shaw Research: New York, 2009.
42. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 5179-97
43. Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98, 10089-92
44. Shao, Y.; Molnar, L. F.; Jung, Y.; Kussmann, J.; Ochsenfeld, C.; Brown, S. T.; Gilbert, A. T. B.; Slipchenko, L. V.; Levchenko, S. V.; O'Neill, D. P.; DiStasio, R. A., Jr.; Lochan, R. C.; Wang, T.; Beran, G. J. O.; Besley, N. A.; Herbert, J. M.; Lin, C. Y.; Van Voorhis, T.; Chien, S. H.; Sodt, A.; Steele, R. P.; Rassolov, V. A.; Maslen, P. E.; Korambath, P. P.; Adamson, R. D.; Austin, B.; Baker, J.; Byrd, E. F. C.; Dachsel, H.; Doerksen, R. J.; Dreuw, A.; Dunietz, B. D.; Dutoi, A. D.; Furlani, T. R.; Gwaltney, S. R.; Heyden, A.; Hirata, S.; Hsu, C.-P.; Kedziora, G.; Khalliulin, R. Z.; Klunzinger, P.; Lee, A. M.; Lee, M. S.; Liang, W.; Lotan, I.; Nair, N.; Peters, B.; Proynov, E. I.; Pieniazek, P. A.; Rhee, Y. M.; Ritchie, J.; Rosta, E.; Sherrill, C. D.; Simmonett, A. C.; Subotnik, J. E.; Woodcock, H. L., III; Zhang, W.; Bell, A. T.; Chakraborty, A. K.; Chipman, D. M.; Keil, F. J.; Warshel, A.; Hehre, W. J.; Schaefer, H. F., III; Kong, J.; Krylov, A. I.; Gill, P. M. W.; Head-Gordon, M. Phys. Chem. Chem. Phys. 2006, 8, 3172-91
45. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. J. Comput. Chem. 1983, 4, 187-217
46. Bouzida, D.; Swendsen, R. H.; Kollman, P. A.; Rosenberg, J. M. J. Comput. Chem. 1992, 13, 1011-21
47. Li, Y.; Breaker, R. R. J. Am. Chem. Soc. 1999, 121, 5364-72
48. Nakano, S.; Cerrone, A. L.; Bevilacqua, P. C. Biochemistry 2003, 42, 2982-94
49. Velikyan, I.; Acharya, S.; Trifonova, A.; Földesi, A.; Chattopadhyaya, J. J. Am. Chem. Soc. 2001, 123, 2893-94
50. Schowen, B. K.; Schowen, R. L. Methods Enzymol. 1982, 87, 551-606
51. Nakano, S.; Bevilacqua, P. C. Biochemistry 2007, 46, 3001-12
52. Nakano, S.; Bevilacqua, P. C. J. Am. Chem. Soc. 2001, 123, 11333-34
53. Anslyn, E.; Breslow, R. J. Am. Chem. Soc. 1989, 111, 4473-82
54. Kobayashi, R. J. Phys. Chem. A 1998, 102, 10813-17
55. Šponer, J.; Leszczynski, J.; Hobza, P. Biopolymers 2001, 61, 3-31
56. McConnell, B. Biochemistry 1978, 17, 3168-76
57. McConnell, B.; Politowski, D. Biophys. Chem. 1984, 20, 135-48
58. Guéron, M.; Leroy, J.-L. Methods Enzymol. 1995, 261, 383-413
59. Davies, J. E.; Doltsinis, N. L.; Kirby, A. J.; Roussev, C. D.; Sprik, M. J. Am. Chem. Soc. 2002, 124, 6594-99
60. Lopez, X.; Schaefer, M.; Dejaegere, A.; Karplus, M. J. Am. Chem. Soc. 2002, 124, 5010-18
61. Wilcox, J. L.; Ahluwalia, A. K.; Bevilacqua, P. C. Acc. Chem. Res. 2011, 44, 1270-79
62. Ke, A.; Ding, F.; Batchelor, J. D.; Doudna, J. A. Structure 2007, 15, 281-87
63. Grotthuss, C. Ann. Chim. 1806, 58, 54-73
64. Agmon, N. Chem. Phys. Lett. 1995, 244, 456-62