An All-Atom Empirical Energy Function for the Simulation of Nucleic Acids

Journal of the American Chemical Society

Volumn 117, Issue 48, 1995, Pages 11946-11975

  MacKerell, Alexander D ^a,b   Wiórkiewicz Kuczera, Joanna ^a   Karplus, Martin ^a  

^a HARVARD UNIVERSITY   (United States)

^b UNIVERSITY OF MARYLAND SCHOOL OF PHARMACY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 6344260593     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja00153a017     Document Type: Article

References (126)

1. Allen, M.P.; Tildesley, D.J. Computer Simulation of Liquids; Clarendon Press: Oxford, 1987.
2. Brooks, C.L., III; Karplus, M.; Pettitt, B.M. Proteins: A Theoretical Perspective of Dynamics, Structure and Thermodynamics’, Wiley Series on Advances in Chemical Physics; Prigognine, I., Rice, S., Eds.; John Wiley & Sons: New York, 1988; Vol. LXXI.
3. Brooks, B.R.; Bruccoleri, R.E.; Olafson, B.D.; States, D.J.; Swaminathan, S.; Karplus, M. J. Comp. Chem. 1983, 4, 187—217.
4. Weiner, S.J.; Kollman, P.A.; Case, D.A.; Singh, U.C.; Ghio, C.; Alagona, G.; Profeta, S., Jr.; Weiner, P. J. Am. Chem. Soc. 1984, 106, 765—784.
5. Weiner, S.J.; Kollman, P.A.; Nguyen, D.T.; Case, D.A. J. Comp. Chem. 1986, 7, 230–252.
6. Nilsson, L.; Karplus, M. J. Comp. Chem. 1986, 7, 591–616.
7. Jorgensen, W.L.; Tirado-Rives, J. J. Am. Chem. Soc. 1988, 110, 1657–1666.
8. Tidor, B.; Irikura, K.K.; Brooks, B.R.; Karplus, M. J. Biomol. Struct. Dyn. 1983, 1, 231–252.
9. Srinivasan, J.; Withka, J.M.; Beveridge, D.L. Biophys. J. 1990, 58, 533–547.
10. Rao, S.N.; Kollman, P. Biopolymers 1990, 29, 517–532.
11. Fritsch, V.; Westhof, E. J. Comp. Chem. 1991, 12, 147–166.
12. Nilsson, L.; Clore, G.M.; Gronenborn, A.M.; Brunger, A.T.; Karplus, M. J. Mol. Biol. 1986, 188, 455–475.
13. Nikonowicz, E.P.; Meadows, R.P.; Fagan, P.; Gorenstein, D.G. Biochemistry 1991, 30, 1323–1334.
14. Keepers, J.W.; Kollman, P.A.; Weiner, P.; James, T.L. Proc. Natl. Acad. Sci. U.S.A. 1982, 79, 5537–5541.
15. Levitt, M. Cold Spring Harbor Symp. Quant. Biol. 1983, 47, 251—275.
16. Tidor, B.; Irikura, K.K.; Brooks, B.R.; Karplus, M. J. Biomol. Struct. Dyn. 1983, 1, 231—252.
17. Westhof, E.; Chevrier, B.; Gallion, S.L.; Weiner, P.K.; Levy, R.M. J. Mol. Biol. 1986, 190, 699–712.
18. Seibel, G.L.; Singh, U.C.; Kollman, P.A. Proc. Natl. Acad. Sci. U.S.A. 1985, 82, 6537–6540.
19. Swamy, K.N.; Clementi, E. Biopolymers 1987, 26, 1901—1927.
20. Laaksonen, A.; Nilsson, L.; Schneider, C.; Guschlbauer Nucleic Acid Res. 1989, 6, 2831–2837.
21. Jung, S.-H. Simulation of DNA and its Interaction with Ligands, Ph.D. Thesis, Harvard University, Department of Chemistry, 1989.
22. Veal, J.M.; Gao, X.; Brown, F.K. J. Am. Chem. Soc. 1993, 115, 7139–7145.
23. Srinivasan, J.; Withka, J.M.; Beveridge, D.L. Biophys. J. 1990, 58, 533–547.
24. Fritsch, V.; Westhof, E. J. Am. Chem. Soc. 1991, 113, 8271–8277.
25. Ravishanker, G.; Swaminathan, S.; Beveridge, D.L.; Lavery, R.; Sklenar, H. J. Biomol. Struct. Dyn. 1989, 6, 669—699.
26. McConnell, K.J.; Nirmala, R.; Young, M.A.; Ravishankar, G.; Beveridge, D.L. J. Am. Chem. Soc. 1994, 116, 4461–4462.
27. Smith, P.E.; Pettitt, B.M. J. Phys. Chem. 1994, 98, 9700–9711.
28. Reiher, W.; Karplus, M. Unpublished.
29. Allen, F.H.: Bellard, S.; Brice, M.D.; Cartwright, B.A.; Doubleday, A.; Higgs, H.; Hummelink, T.; Hummelink-Peters, B.G.; Kennard, O.; Motherwell, W.D.S.; Rodgers, J.R.: Watson, D.G. Acta Crystallogr. 1979.
30. Taylor, R.; Kennard, O. J. Mol. Struct. 1982, 78, 1—28.
31. Jorgensen, W.L.: Chandrasekhar, J.; Madura, J.D.; Impey, R.W.; Klein, M.L. J. Chem. Phys. 1983, 79, 926–935.
32. Reiher, W.E., III Ph.D. Thesis, Department of Chemistry, Harvard University, 1985.
33. MacKerell, A.D., Jr.; Fischer, S.; Field, M.J.; Watanabe, M.; Karplus, M. Manuscript in preparation.
34. Singh, U.C.; Kollman, P.A. J. Comp. Chem. 1984, 5, 129—145.
35. Chirlian, L.E.; Francl, M.M. J. Comp. Chem. 1987, 8, 894–905.
36. Bayly, C.I.; Cieplak, P.; Cornell, W.D.; Kollman, P.A. J. Phys. Chem. 1993, 97, 10269–10280.
37. MacKerell, A.D., Jr.; Karplus, M. J. Phys. Chem. 1991, 95, 10559–10560.
38. Jorgensen, W.L.; Swenson, C.J. J. Am. Chem. Soc. 1985, 107, 569–587.
39. Jorgensen, W.L. J. Phys. Chem. 1986, 90, 1276–1284.
40. Warshel, A.; Lifson, S. J. Chem. Phys. 1970, 53, 582–594.
41. MacKerell, A.D., Jr.; Karplus, M. Manuscript in preparation.
42. Rosenberg, J.M.; Seeman, N.C.; Day, R.O.; Rich, A. J. Mol. Biol. 1976, 104, 145–167.
43. Privé, G.G.; Yanagi, R.; Dickerson, R.E. J. Mol. Biol. 1991, 217, 177–199.
44. Gessnet, R.V.; Quigley, G.J.; Wang, A.H.-J.; van der Marel, G.; van Boom, J.H.; Rich, A. Biochemistry 1985, 24, 237–240.
45. Pettitt, B.M.; Karplus, M. J. Am. Chem. Soc. 1985, 107, 1166—1173.
46. Smith, J.C.; Karplus, M. J. Am. Chem. Soc. 1992, 114, 801–812.
47. Fischer, W.; Brickmann, J. Ber. Bunsenges. Phys. Chem. 1982, 86, 650.
48. Kuczera, K.; Wiórkiewicz-Kuczera, J. The MOLVIB Program.
49. Hagler, A.T.; Huler, E.; Lifson, S. J. Am. Chem. Soc. 1974, 96, 5319–5327.
50. Berendsen, H.J.C.; Postma, J.P.M.; van Gunsteren, W.F.; DiNola, A.; Haak, J.R. J. Chem. Phys. 1984, 81, 3684–3690.
51. Ryckaert, J.P.; Cicotti, G.; Berendsen. H.J.C. J. Chem. Phys. 1977, 23, 327–341.
52. Brünger, A.T.; Karplus. M. Proteins 1988, 4, 148–156.
53. Seibel, G.L.; Singh, U.C.; Kollman, P.A. Proc. Natl. Acad. Sci. U.S.A. 1985, 82, 6537–6540.
54. Binkley, J.S.; Frisch, M.; Krishnam, R.; DeFrees, D.J.; Schlegel, H.B.; Whiteside, R.A.; Fluder, E.; Seeger, R.; Pople, J.A. GAUSSIAN 82, Releases A and H; Carnegie-Mellon University; Frisch, M.J.; Binkley, J.S.; Schlegel, H.B.; Raghavachari, K.; Melius, C.F.; Martin, R.L.; Stewart, J.J.P.; Bobrowicz, F.W.; Rohlfing, C.M.; Kahn, L.R.; Defrees, D.J.; Seeger, R.; Whitesides, R.A.; Fox, D.J.; Fleuder, E.M.; Pople, J.A. Gaussian 86, Carnegie-Mellon Quantum Chemistry Publishing Unit: Pittsburgh, PA, 1984.
55. Hirato, E.; Sugisake, R.; Nielsen, C.J.; Sórensen, G.O. J. Mol. Spectrosc. 1974, 53, 62—76.
56. Gao, J.; Jorgensen, W.L. Personal communication.
57. Aida, M. J. Comp. Chem. 1988, 9, 362—368.
58. Derreamaux, P.; Vergoten, G.; Lagant, P. J. Comp. Chem. 1990, 11, 560–568.
59. Barnes, A.J.; Stuckey, M.A.; LeGall, L. Spectrochim. Acta 1984, 40A, 419–431.
60. Harsanyi, L.; Csaszar, P.; Csaszar, A.; Boggs, J.E. Int. J. Quantum Chem. 1986, 29, 799–815.
61. Szczesniak, M.; Nowak, M.J.; Rostkowska, H.; Szczepaniak, K.; Person, W.B.; Shugar, D. J. Am. Chem. Soc. 1983, 105, 5969–5976.
62. Graindourze. M.; Smets, J.; Zeegers-Huyskens, Th.; Maes, G. J. Mol. Struct. 1990, 222, 345–364.
63. Nowak, M.J. J. Mol. Struct. 1989, 193, 35–49.
64. Mathlouthi, M.; Seuvre, A.-M.; Koenig, J.L. Carbohydr. Res. 1984, 134, 23–38.
65. Szczesniak, M.; Szczepaniak, K.; Kwiatkowski, J.S.; KuBulat, K.; Person, W.B. J. Am. Chem. Soc. 1988, 110, 8319–8330.
66. Radchenko, E.D.; Sheina, G.G.; Smorygo, N.A.; Blagoi, Yu. P. J. Mol. Struct. 1984, 116, 387–396.
67. Wiorkiewicz-Kuczera, J.; Karplus, M. J. Am. Chem. Soc. 1990. 112, 5324–5340.
68. Nowak, M.J.; Lapinski, L.; Kwiatkowski, J.S.; Leszczynski, J. Spectrochim. Acta 1991, 47A, 87—103.
69. Leszczynski, J. Int. J. Quantum Chem. Quantum Biol. Symp. 1992, 19, 43.
70. Stepanian, S.G.; Sheina, G.G.; Radchenko, E.D.; Blagoi, Yu. P. J. Mol. Struct. 1985, 131, 333.
71. Majoube, M.J. Raman Spectrosc. 1985, 16, 98.
72. Szczepaniak, K.; Szczesniak, M. J. Mol. Struct. 1987, 156, 29–42.
73. Latajka, Z.; Person, W.B.; Morokuma, K. J. Mol. Struct. (THEOCHEM) 1986, 135, 253–266.
74. Seeman, N.C.; Rosenberg, J.M.; Suddath, F.L.; Kim, J.J.P.; Rich, A. J. Mol. Biol. 1976, 104, 109–144.
75. Gelin, B.R.; Karplus, M. Proc. Natl. Acad. Sci. U.S.A. 1975, 72, 2002–2006.
76. Pranata, J.; Wierschke, S.G.; Jorgensen W.L. J. Am. Chem. Soc. 1991, 113, 2810–2819.
77. Yanson, I.K.; Teplitsky, A.B.; Sukhodub, L.F. Biopolymers 1979, 18, 1149–1170.
78. Frey, M.N.; Koetzle, T.F.; Lehmann, M.S.; Hamilton, W.C. J. Chem. Phys. 1973, 59, 915–924.
79. Cornell, W.D.; Cieplak, P.; Bayly, C.I.; Kollman, P.A. J. Am. Chem. Soc. 1993, 115, 9620–9631.
80. Gould, I.R.; Kollman, P.A. J. Am. Chem. Soc. 1994, 116, 2493–2499.
81. DeVoe, H.; Tinoco, I., Jr. J. Mol. Biol. 1962, 4, 500.
82. Brown, R.B.; Godfrey, P.D.; McNaughton, D.; Pierlot, A.P. J. Am. Chem. Soc. 1988, 110, 2329–2330.
83. Pearlman, D.A.; Kim, S.-H. J. Mol. Biol. 1990, 211, 171–187.
84. Drew, H.R.; Wing, R.M.; Takano, T.; Broka, S.; Tanaka, S.; Itakura, K.; Dickerson, R.E. Proc. Natl. Acad. Sci. U.S.A. 1981, 78, 2179.
85. Aida, M.; Nagata, C. Int. J. Quantum Chem. 1986, 29, 1253—1261.
86. Aida, M. J. Theor. Biol. 1988, 130, 327–335.
87. Arnott, S.; Hukins, D.W.L. J. Mol. Biol. 1973, 81, 93–105.
88. Suurkuusk, J.; Alvarez, J.; Freire, E.; Biltonen, R. Biopolymers 1977, 16, 2641–2652.
89. Marky, L.A.; Breslauer, K. J. Biopolymers 1982, 21, 2185–2194.
90. Petersheim, M.; Turner, D.H. Biochemistry 1983, 22, 256—263.
91. Ornstein, R.L.; Rein, R.; Breen, D.L.; Macelroy, R.D. Biopolymers 1978, 17, 2341.
92. Haram, T.E.; Berkovich-Yellin, Z.; Shakked, Z. J. Biomol. Struct. Dyn. 1984, 2, 397.
93. Hoogsteen, K. Acta Crystallogr. 1963, 16, 28–38.
94. Stewart, R.F.; Jensen, L.H. J. Chem. Phys. 1964, 40, 2071—2075.
95. Stewart, R.F.; Jensen, L.H. Acta Crystallogr. 1967, 23, 1102—1105.
96. O’Brien, E.J. Acta Crystallogr. 1967, 23, 92—106.
97. MacKerell, A.D., Jr.; Karplus, M. Manuscript in preparation.
98. Norberg, J.; Nilsson, L. Personal comunication.
99. Garrigou, C.; Bouloussa, O.; Clement, C. Can. J. Spectrosc. 1976, 21, 75–82.
100. Liang, C.; Ewig, C.S.; Stouch, T.R.; Hagler, A.T. J. Am. Chem. Soc. 1993, 115, 1537.
101. Jayaram, B.; Ravishanker, G.; Beveridge, D.L. J. Phys. Chem. 1988, 92, 1032–1034.
102. Schlenkrich, M. Ph.D. Thesis, Department of Chemistry, Darmstadt Technical High School, Germany, 1992.
103. Jayaram, B.; Mezei, M.; Beveridge, D.L. J. Comp. Chem. 1987, 8, 917–942.
104. MacKerell, A.D., Jr.; Sommer, M.S.; Karplus, J. Mol. Biol. 1995, 247, 774–807.
105. Hehre, W.J.; Radom, L.; Schleyer, P.R.; Pople, T.A. Ab Initio Molecular Orbital Theory: John Wiley & Sons: New York, 1986.
106. Kuczera, K.; MacKerell, A.D., Jr.; Gao, J.; Karplus, M. Manucript in preparation.
107. Gao, J. Ph.D. Thesis, Purdue University, Department of Chemistry, 1987.
108. Slater, J.C.; Kirkwood, J.G. Phys. Rev. 1931, 37, 682.
109. Pitzer, K.S. In Advances in Chemical Physics: Prigogine, I., Ed.; Interscience: New York, 1959; Vol. 2.
110. Nguyen, D.; Lau, F.T.K.; MacKerell, A.D., Jr.; Karplus, M. Manuscript in preparation.
111. Arnott, S.; Hukins, D.W.L. Biochem. J. 1972, 130, 453–465.
112. de Leeuw, H.P.M.; Haasnoot, C.A.G.; Altoona, C. Isr. J. Chem. 1980, 20, 108–126.
113. Olsen, W.K.; Sussman, J.L. J. Am. Chem. Soc. 1982, 104, 270—278.
114. Olsen, W.K. J. Am. Chem. Soc. 1982, 104, 278–286.
115. Jung, S.-H.; MacKerell, A.D., Jr.; Karplus, M. Manuscript in preparation.
116. Saenger, W. Principles of Nucleic Acid Structure; Springer-Verlag: New York, 1983.
117. Altona, C.; Sundaralingam, M. J. Am. Chem. Soc. 1972, 94, 8205—8212.
118. Subramanian, P.S.; Pitchumani, S.; Beveridge, D.L.; Berman, H.M. Biopolymers 1990. 29, 771.
119. Dickerson, R.E.; Kopka, M.L.; Drew, H.R. Structural Correlations in B-DNA. In Structre and Dynamics: Nucleic Acids and Proteins: Clement, E., Sarma, R.H., Eds.; Adenine Press: New York, 1982.
120. Prod’hom, B.; Karplus, M. Manuscript in preparation.
121. Singh, U.C.; Weiner, S.J.; Kollman, P. Proc. Natl. Acad. Sci. U.S.A. 1985, 82, 755–759.
122. van Gunsteren, W.F.; Berendsen, H.J.C. Groningen Molecular Simulations System, BIOMOS B.V., Laboratory of Physical Chemistry, University of Groningen, Groningen, The Netherlands, 1986.
123. Zielinski, T.J.; Shibata, M. Biopolymers 1990, 29, 1027–1044.
124. Swaminathan, S.; Ravishanker, G.; Beveridge, D.L. J. Am. Chem. Soc. 1991, 113, 5027–5040.
125. Miaskiewicz, K.; Osman, R.; Weinstein, H. J. Am. Chem. Soc. 1993, 115, 1526.
126. Roux, B. Ph.D. Thesis, Chemistry Department, Harvard University, 1989.