How to understand quantum chemical computations on DNA and RNA systems? A practical guide for non-specialists

Methods

Volumn 64, Issue 1, 2013, Pages 3-11

  Šponer, Jiří ^a,b   Šponer, Judit E ^a,b   Mládek, Arnošt ^a,b   Banáš, Pavel ^a,c   Jurečka, Petr ^c   Otyepka, Michal ^a,c  

^a INSTITUTE OF BIOPHYSICS   (Czech Republic)

^b CENTRAL EUROPEAN INSTITUTE OF TECHNOLOGY   (Czech Republic)

^c PALACKÝ UNIVERSITY   (Czech Republic)

Author keywords

DNA structure; Molecular mechanics; Molecular structures and energies; Quantum chemistry

Indexed keywords

DNA; NUCLEIC ACID; RNA;

ARTICLE; CALCULATION; CHEMICAL STRUCTURE; DENSITY FUNCTIONAL THEORY; DNA DETERMINATION; DNA STRUCTURE; HUMAN; MOLECULAR MECHANICS; PRIORITY JOURNAL; QUANTUM CHEMISTRY; RNA ANALYSIS; SIMULATION;

DNA STRUCTURE; MOLECULAR MECHANICS; MOLECULAR STRUCTURES AND ENERGIES; QUANTUM CHEMISTRY;

COMPUTER SIMULATION; DNA; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; NUCLEIC ACID CONFORMATION; RNA;

EID: 84886237370     PISSN: 10462023     EISSN: 10959130     Source Type: Journal    
DOI: 10.1016/j.ymeth.2013.05.025     Document Type: Article

References (133)

1. Sponer J., Lankas F. Computational Studies of RNA and DNA 2006, Springer, Dordrecht.
2. Schlick T., Neidle S. Innovations in Biomolecular Modeling and Simulations 2012, Royal Society of Chemistry.
3. Cheatham T.E., Miller J.L., Fox T., Darden T.A., Kollman P.A. J. Am. Chem. Soc. 1995, 117:4193-4194.
4. LouiseMay S., Auffinger P., Westhof E. Curr. Opin. Struct. Biol. 1996, 6:289-298.
5. Darden T., York D., Pedersen L. J. Chem. Phys. 1993, 98:10089-10092.
6. Perez A., Luque F.J., Orozco M. J. Am. Chem. Soc. 2007, 129:14739-14745.
7. Reshetnikov R., Golovin A., Spiridonova V., Kopylov A., Sponer J. J. Chem. Theory Comput. 2010, 6:3003-3014.
8. Sklenovsky P., Florova P., Banas P., Reblova K., Lankas F., Otyepka M., Sponer J. J. Chem. Theory Comput. 2011, 7:2963-2980.
9. Dror R.O., Dirks R.M., Grossman J.P., Xu H.F., Shaw D.E. Annu. Rev. Biophys. 2012, 49:429-452.
10. Mlynsky V., Banas P., Hollas D., Reblova K., Walter N.G., Sponer J., Otyepka M. J. Phys. Chem. B 2010, 114:6642-6652.
11. Besseova I., Banas P., Kuhrova P., Kosinova P., Otyepka M., Sponer J. J. Phys. Chem. B 2012, 116:9899-9916.
12. Cheatham T.E. Curr. Opin. Struct. Biol. 2004, 14:360-367.
13. Banas P., Hollas D., Zgarbova M., Jurecka P., Orozco M., Cheatham T.E., Sponer J., Otyepka M. J. Chem. Theory Comput. 2010, 6:3836-3849.
14. Ditzler M.A., Otyepka M., Sponer J., Walter N.G. Acc. Chem. Res. 2010, 43:40-47.
15. Sponer J., Hobza P. J. Phys. Chem. 1994, 98:3161-3164.
16. Gould I.R., Kollman P.A. J. Am. Chem. Soc. 1994, 116:2493-2499.
17. Sponer J., Gabb H.A., Leszczynski J., Hobza P. Biophys. J. 1997, 73:76-87.
18. Hobza P., Sponer J., Polasek M. J. Am. Chem. Soc. 1995, 117:792-798.
19. Sponer J., Leszczynski J., Hobza P. J. Phys. Chem. 1996, 100:5590-5596.
20. Sponer J., Leszczynski J., Hobza P. J. Phys. Chem. 1996, 100:1965-1974.
21. Bondarev D.A., Skawinski W.J., Venanzi C.A. J. Phys. Chem. B 2000, 104:815-822.
22. Hobza P., Sponer J. Chem. Rev. 1999, 99:3247-3276.
23. Sponer J., Leszczynski J., Hobza P. Biopolymers 2001, 61:3-31.
24. Hobza P., Sponer J. J. Am. Chem. Soc. 1808, 124(2002):11802-11808.
25. Sponer J., Jurecka P., Marchan I., Luque F.J., Orozco M., Hobza P. Chem. Eur. J. 2006, 12:2854-2865.
26. Leininger M.L., Nielsen I.M.B., Colvin M.E., Janssen C.L. J. Phys. Chem. A 2002, 106:3850-3854.
27. Sponer J., Riley K.E., Hobza P. Phys. Chem. Chem. Phys. 2008, 10:2595-2610.
28. Nir E., Kleinermanns K., de Vries M.S. Nature 2000, 408:949-951.
29. Nir E., Janzen C., Imhof P., Kleinermanns K., de Vries M.S. Phys. Chem. Chem. Phys. 2002, 4:732-739.
30. Banas P., Jurecka P., Walter N.G., Sponer J., Otyepka M. Methods 2009, 49:202-216.
31. Hill J.G., Platts J.A. J. Chem. Theory Comput. 2007, 3:80-85.
32. Hongo K., Cuong N.T., Maezono R. J. Chem. Theory Comput. 2013, 9:1081-1086.
33. Austin B.M., Zubarev D.Y., Lester W.A. Chem. Rev. 2012, 112:263-288.
34. Grimme S. J. Comput. Chem. 2004, 25:1463-1473.
35. Grimme S. WIREs Comput. Mol. Sci. 2011, 1:211-228.
36. Riley K.E., Pitonak M., Jurecka P., Hobza P. Chem. Rev. 2010, 110:5023-5063.
37. Sponer J., Mladek A., Sponer J.E., Svozil D., Zgarbova M., Banas P., Jurecka P., Otyepka M. Phys. Chem. Chem. Phys. 2012, 14:15257-15277.
38. Sponer J., Sponer J.E., Petrov A.I., Leontis N.B. J. Phys. Chem. B 2010, 114:15723-15741.
39. Mladek A., Sponer J.E., Jurecka P., Banas P., Otyepka M., Svozil D., Sponer J. J. Chem. Theory Comput. 2010, 6:3817-3835.
40. Zhao Y., Truhlar D.G. Theor. Chem. Acc. 2008, 120:215-241.
41. Klimes J., Bowler D.R., Michaelides A. J. Phys. Condens. Matter 2010, 22:2201-2205.
42. Granatier J., Lazar P., Otyepka M., Hobza P. J. Chem. Theory Comput. 2011, 7:3743-3755.
43. Klimes J., Bowler D.R., Michaelides A. Physical Review B 2011, 83:195131-195144.
44. Dion M., Rydberg H., Schroder E., Langreth D.C., Lundqvist B.I. Phys. Rev. Lett. 2004, 92:246401-246404.
45. Lazar P., Karlicky F., Jurecka P., Kocman M., Otyepkova E., Safarova K., Otyepka M. J. Am. Chem. Soc. 2013, 135:6372-6377.
46. Cooper V.R., Thonhauser T., Langreth D.C. J. Chem. Phys. 2008, 128:204102-204105.
47. Grimme S., Antony J., Ehrlich S., Krieg H. J. Chem. Phys. 2010, 132:154104-154122.
48. Mladek A., Krepl M., Svozil D., Cech P., Otyepka M., Banas P., Zgarbova M., Jurecka P., Sponer J. Phys. Chem. Chem. Phys. 2013, 15:7295-7310.
49. Mathews D.H., Sabina J., Zuker M., Turner D.H. J. Mol. Biol. 1999, 288:911-940.
50. Mathews D.H., Turner D.H. Curr. Opin. Struct. Biol. 2006, 16:270-278.
51. Bommarito S., Peyret N., SantaLucia J. Nucleic Acids Res. 2000, 28:1929-1934.
52. Protozanova E., Yakovchuk P., Frank-Kamenetskii M.D. J. Mol. Biol. 2004, 342:775-785.
53. Svozil D., Hobza P., Sponer J. J. Phys. Chem. B 2010, 114:1191-1203.
54. Sponer J., Morgado C.A., Svozil D. J. Phys. Chem. B 2012, 116:8331-8332.
55. Siegfried N.A., Kierzek R., Bevilacqua P.C. J. Am. Chem. Soc. 2010, 132:5342-5344.
56. Koller A.N., Bozilovic J., Engels J.W., Gohlke H. Nucleic Acids Res. 2010, 38:3133-3146.
57. Krepl M., Otyepka M., Banas P., Sponer J. J. Phys. Chem. B 2013, 117:1872-1879.
58. Morgado C.A., Svozil D., Turner D.H., Sponer J. Phys. Chem. Chem. Phys. 2012, 14:12580-12591.
59. Yildirim I., Turner D.H. Biochemistry 2005, 44:13225-13234.
60. Kopitz H., Zivkovic A., Engels J.W., Gohlke H. Chembiochem 2008, 9:2619-2622.
61. Luo R., Gilson H.S.R., Potter M.J., Gilson M.K. Biophys. J. 2001, 80:140-148.
62. Jafilan S., Klein L., Hyun C., Florian J. J. Phys. Chem. B 2012, 116:3613-3618.
63. Florian J., Sponer J., Warshel A. J. Phys. Chem. B 1999, 103:884-892.
64. Banas P., Mladek A., Otyepka M., Zgarbova M., Jurecka P., Svozil D., Lankas F., Sponer J. J. Chem. Theory Comput. 2012, 8:2448-2460.
65. Marshall M.S., Burns L.A., Sherrill C.D. J. Chem. Phys. 2011, 135:194102-194111.
66. Sponer J., Jurecka P., Hobza P. J. Am. Chem. Soc. 2004, 126:10142-10151.
67. 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, 117:5179-5197.
68. Sponer J., Cang X., Cheatham T.E. Methods 2012, 57:25-39.
69. Bothe J.R., Nikolova E.N., Eichhorn C.D., Chugh J., Hansen A.L., Al-Hashimi H.M. Nat. Methods 2011, 8:919-931.
70. Limongelli V., DelTito S., Cerofolini L., Fragai M., Pagano B., Trotta R., Cosconati S., Marinelli L., Novellino E., Bertini I., Randazzo A., Luchinat C., Parrinello M. Angew. Chem. Int. Edit. 2013, 52:2269-2273.
71. Kim E., Yang C., Pak Y. J. Chem. Theory Comput. 2012, 8:4845-4851.
72. Kuhrova P., Banas P., Best R.B., Sponer J., Otyepka M. J. Chem. Theory Comput. 2013, 9:2115-2125.
73. Perez A., Marchan I., Svozil D., Sponer J., Cheatham T.E., Laughton C.A., Orozco M. Biophys. J. 2007, 92:3817-3829.
74. Zgarbova M., Otyepka M., Sponer J., Mladek A., Banas P., Cheatham T.E., Jurecka P. J. Chem. Theory Comput. 2011, 7:2886-2902.
75. Tomasi J., Mennucci B., Cammi R. Chem. Rev. 2005, 105:2999-3093.
76. Orozco M., Luque F.J. Chem. Rev. 2000, 100:4187-4225.
77. Grochowski P., Trylska J. Biopolymers 2008, 89:93-113.
78. Homeyer N., Gohlke H. Mol. Inform. 2012, 31:114-122.
79. Kollman P.A., Massova I., Reyes C., Kuhn B., Huo S.H., Chong L., Lee M., Lee T., Duan Y., Wang W., Donini O., Cieplak P., Srinivasan J., Case D.A., Cheatham T.E. Acc. Chem. Res. 2000, 33:889-897.
80. Schutz M., Rauhut G., Werner H.J. J. Phys. Chem. A 1998, 102:5997-6003.
81. Hampel C., Werner H.J. J. Chem. Phys. 1996, 104:6286-6297.
82. Sherrill C.D. Computations of Noncovalent π Interactions, Reviews in Computational Chemistry 2009, John Wiley & Sons, Inc., (pp. 1-38).
83. Dunning T.H. J. Chem. Phys. 1989, 90:1007-1023.
84. Luisi B., Orozco M., Sponer J., Luque F.J., Shakked Z. J. Mol. Biol. 1998, 279:1123-1136.
85. Zgarbova M., Otyepka M., Sponer J., Hobza P., Jurecka P. Phys. Chem. Chem. Phys. 2010, 12:10476-10493.
86. Bock C.W., Katz A.K., Markham G.D., Glusker J.P. J. Am. Chem. Soc. 1999, 121:7360-7372.
87. Dudev T., Lim C. Annual Review of Biophysics 2008, 37:97-116.
88. Dudev T., Lim C. Chem. Rev. 2003, 103:773-787.
89. Munoz J., Sponer J., Hobza P., Orozco M., Luque F.J. J. Phys. Chem. B 2001, 105:6051-6060.
90. Sponer J., Sabat M., Gorb L., Leszczynski J., Lippert B., Hobza P. J. Phys. Chem. B 2000, 104:7535-7544.
91. Sponer J., Burda J.V., Sabat M., Leszczynski J., Hobza P. J. Phys. Chem. A 1998, 102:5951-5957.
92. Petrov A.S., Bernier C.R., Hsiao C.L., Okafor C.D., Tannenbaum E., Stern J., Gaucher E., Schneider D., Hud N.V., Harvey S.C., Williams L.D. J. Phys. Chem. B 2012, 116:8113-8120.
93. Rulisek L., Sponer J. J. Phys. Chem. B 2003, 107:1913-1923.
94. Petrov A.S., Bowman J.C., Harvey S.C., Williams L.D. RNA 2011, 17:291-297.
95. Petrov A.S., Lamm G., Pack G.R. Biopolymers 2005, 77:137-154.
96. Petrov A.S., Pack G.R., Lamm G. J. Phys. Chem. B 2004, 108:6072-6081.
97. Bock C.W., Katz A.K., Glusker J.P. J. Am. Chem. Soc. 1995, 117:3754-3763.
98. Oliva R., Tramontano A., Cavallo L. RNA 2007, 13:1427-1436.
99. Gresh N., Garmer D.R. J. Comput. Chem. 1996, 17:1481-1495.
100. Gresh N., Sponer J.E., Spackova N., Leszczynski J., Sponer J. J. Phys. Chem. B 2003, 107:8669-8681.
101. Bowman J.C., Lenz T.K., Hud N.V., Williams L.D. Curr. Opin. Struct. Biol. 2012, 22:262-272.
102. Baker C.M., Anisimov V.M., MacKerell A.D. J. Phys. Chem. B 2011, 115:580-596.
103. Ponder J.W., Wu C.J., Ren P.Y., Pande V.S., Chodera J.D., Schnieders M.J., Haque I., Mobley D.L., Lambrecht D.S., DiStasio R.A., Head-Gordon M., Clark G.N.I., Johnson M.E., Head-Gordon T. J. Phys. Chem. B 2010, 114:2549-2564.
104. Halgren T.A., Damm W. Curr. Opin. Struct. Biol. 2001, 11:236-242.
105. Zgarbova M., Luque F.J., Sponer J., Otyepka M., Jurecka P. J. Chem. Theory Comput. 2012, 8:3232-3242.
106. Bayly C.I., Cieplak P., Cornell W.D., Kollman P.A. J. Phys. Chem. 1993, 97:10269-10280.
107. Wang J.M., Cieplak P., Kollman P.A. J. Comput. Chem. 2000, 21:1049-1074.
108. Cieplak P., Cornell W.D., Bayly C., Kollman P.A. J. Comput. Chem. 1995, 16:1357-1377.
109. Dupradeau F.Y., Pigache A., Zaffran T., Savineau C., Lelong R., Grivel N., Lelong D., Rosanski W., Cieplak P. Phys. Chem. Chem. Phys. 2010, 12:7821-7839.
110. Mackerell A.D., Wiorkiewiczkuczera J., Karplus M. J. Am. Chem. Soc. 1975, 117(1995):11946-11975.
111. MacKerell A.D., Banavali N.K. J. Comput. Chem. 2000, 21:105-120.
112. Krepl M., Zgarbova M., Stadlbauer P., Otyepka M., Banas P., Koca J., Cheatham T.E., Jurecka P., Sponer J. J. Chem. Theory Comput. 2012, 8:2506-2520.
113. Hart K., Foloppe N., Baker C.M., Denning E.J., Nilsson L., MacKerell A.D. J. Chem. Theory Comput. 2012, 8:348-362.
114. Denning E.J., Priyakumar U.D., Nilsson L., Mackerell A.D. J. Comput. Chem. 2011, 32:1929-1943.
115. Zgarbova M., Luque F.J., Sponer J., Cheatham T.E., Otyepka M., Jurecka P. J. Chem. Theory Comput. 2013, 9:2339-2354.
116. Yildirim I., Kennedy S.D., Stern H.A., Hart J.M., Kierzek R., Turner D.H. J. Chem. Theory Comput. 2012, 8:172-181.
117. Yildirim I., Stern H.A., Kennedy S.D., Tubbs J.D., Turner D.H. J. Chem. Theory Comput. 2010, 6:1520-1531.
118. Warshel A., Levitt M. J. Mol. Biol. 1976, 103:227-249.
119. Garrec J., Patel C., Rothlisberger U., Dumont E. J. Am. Chem. Soc. 2012, 134:2111-2119.
120. Gkionis K., Mutter S.T., Platts J.A. RSC Adv. 2013, 3:4066-4073.
121. Vlieghe D., Sponer J., Van Meervelt L. Biochemistry 1999, 38:16443-16451.
122. Zirbel C.L., Sponer J.E., Sponer J., Stombaugh J., Leontis N.B. Nucleic Acids Res. 2009, 37:4898-4918.
123. Sponer J., Mokdad A., Sponer J.E., Spackova N., Leszczynski J., Leontis N.B. J. Mol. Biol. 2003, 330:967-978.
124. Meyer M., Steinke T., Brandl M., Suhnel J. J. Comput. Chem. 2001, 22:109-124.
125. Guerra C.F., Bickelhaupt F.M., Snijders J.G., Baerends E.J. J. Am. Chem. Soc. 2000, 122:4117-4128.
126. Parker T.M., Hohenstein E.G., Parrish R.M., Hud N.V., Sherrill C.D. J. Am. Chem. Soc. 2012, 135:1306-1316.
127. Lech C.J., Heddi B., Phan A.T. Nucleic Acids Res. 2013, 41:2034-2046.
128. Zhao Y., Truhlar D.G. Acc. Chem. Res. 2008, 41:157-167.
129. Ehrlich S., Moellmann J., Grimme S. Acc. Chem. Res. 2013, 46:916-926.
130. J. Sponer, A. Mladek, N. Spackova, X.H. Cang, T.E. Cheatham III, S. Grimme, J. Am. Chem. Soc. 135 (2013) in press, http://dx.doi.org/10.1021/ja402525c.
131. Cang X.H., Sponer J., Cheatham T.E. Nucleic Acids Res. 2011, 39:4499-4512.
132. Svozil D., Kalina J., Omelka M., Schneider B. Nucleic Acids Res. 2008, 36:3690-3706.
133. Halkier A., Helgaker T., Jorgensen P., Klopper W., Olsen J. Chem. Phys. Lett. 1999, 302:437-446.