Prediction of RNA multiloop and pseudoknot conformations from a lattice-based, coarse-grain tertiary structure model

Journal of Chemical Physics

Volumn 132, Issue 9, 2010, Pages

  Jost, Daniel ^a   Everaers, Ralf ^a  

^a UNIVERSITÉ DE LYON   (France)

Author keywords

[No Author keywords available]

Indexed keywords

PHYSICAL CHEMISTRY; PHYSICS;

ATTRACTIVE INTERACTIONS; CHAIN CONNECTIVITY; COMPLEX STRUCTURE; ELEMENTARY STRUCTURE; NATIVE STRUCTURES; SECONDARY STRUCTURAL ELEMENTS; SECONDARY STRUCTURES; TERTIARY STRUCTURES;

RNA;

RNA;

ALGORITHM; ARTICLE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; CONFORMATION; ULTRASTRUCTURE;

ALGORITHMS; COMPUTER SIMULATION; MODELS, CHEMICAL; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; RNA;

EID: 77949395973     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3330906     Document Type: Article

References (109)

1. C. Calladine, H. Drew, B. Luisi, and A. Travers, Understanding DNA: The Molecule and How It Works (Elsevier, San Diego, 2004).
2. R. Gesteland, T. R. Cech, and J. F. Atkins, RNA World (Cold Spring Harbor Laboratory, New York, 2005).
3. A. Fire, S. Xu, M. K. Montgomery, S. A. Kostas, S. E. Driver, and C. C. Mello, Nature (London) NATUAS 0028-0836 391, 806 (1998). 10.1038/35888
4. D. D. Shoemaker, E. E. Schadt, C. D. Armour, Y. D. He, P. Garrett-Engele, P. D. McDonagh, P. M. Loerch, A. Leonardson, P. Y. Lum, G. Cavet, L. F. Wu, S. J. Altschuler, S. Edwards, J. King, J. S. Tsang, G. Schimmack, J. M. Schelter, J. Koch, M. Ziman, M. J. Marton, B. Li, P. Cundiff, T. Ward, J. Castle, M. Krolewski, M. R. Meyer, M. Mao, J. Burchard, M. J. Kidd, H. Dai, J. W. Phillips, P. S. Linsley, R. Stoughton, S. Scherer, and M. S. Boguski, Nature (London) NATUAS 0028-0836 409, 922 (2001). 10.1038/35057141
5. N. C. Seeman, Biochemistry BICHAW 0006-2960 42, 7259 (2003). 10.1021/bi030079v
6. P. W. K. Rothemund, Nature (London) NATUAS 0028-0836 440, 297 (2006). 10.1038/nature04586
7. B. A. Shapiro, Y. G. Yingling, W. Kasprzak, and E. Bindewald, Curr. Opin. Struct. Biol. COSBEF 0959-440X 17, 157 (2007). 10.1016/j.sbi.2007.03.001
8. E. Capriotti and M. A. Marti-Renom, Curr. Bioinformatics 3, 32 (2008). 10.2174/157489308783329823
9. D. H. Mathews, J. Sabina, M. Zuker, and D. H. Turner, J. Mol. Biol. JMOBAK 0022-2836 288, 911 (1999). 10.1006/jmbi.1999.2700
10. D. H. Mathews, M. D. Disney, J. L. Childs, S. J. Schroeder, M. Zuker, and D. H. Turner, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 101, 7287 (2004). 10.1073/pnas.0401799101
11. M. Zuker, Nucleic Acids Res. NARHAD 0305-1048 31, 3406 (2003). 10.1093/nar/gkg595
12. N. R. Markham and M. Zuker, Nucleic Acids Res. NARHAD 0305-1048 33, W577 (2005). 10.1093/nar/gki591
13. I. L. Hofacker, Nucleic Acids Res. NARHAD 0305-1048 31, 3429 (2003). 10.1093/nar/gkg599
14. E. Rivas and S. R. Eddy, J. Mol. Biol. JMOBAK 0022-2836 285, 2053 (1999). 10.1006/jmbi.1998.2436
15. S. Cao and S. J. Chen, RNA RNARFU 1355-8382 11, 1884 (2005). 10.1261/rna.2109105
16. T. R. Einert, P. Nager, H. Orland, and R. R. Netz, Phys. Rev. Lett. PRLTAO 0031-9007 101, 048103 (2008). 10.1103/PhysRevLett.101.048103
17. A. P. Gultyaev, F. H. van Batenburg, and C. W. Pleij, J. Mol. Biol. JMOBAK 0022-2836 250, 37 (1995). 10.1006/jmbi.1995.0356
18. B. A. Shapiro, W. Kasprzak, C. Grunewald, and J. Aman, J. Mol. Graphics Modell. JMGMFI 1093-3263 25, 514 (2006). 10.1016/j.jmgm.2006.04.004
19. H. Isambert and E. D. Siggia, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 97, 6515 (2000). 10.1073/pnas.110533697
20. A. Xayaphoummine, T. Bucher, F. Thalmann, and H. Isambert, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 100, 15310 (2003). 10.1073/pnas.2536430100
21. A. Xayaphoummine, T. Bucher, F. Thalmann, and H. Isambert, Nucleic Acids Res. NARHAD 0305-1048 33, W605 (2005). 10.1093/nar/gki447
22. Y. G. Yingling and B. A. Shapiro, J. Mol. Graphics Modell. JMGMFI 1093-3263 25, 261 (2006). 10.1016/j.jmgm.2006.01.003
23. J. Burks, C. Zwieb, F. Muler, I. Wower, and J. Wower, BMC Mol. Biol. 1471-2199 6, 14 (2005). 10.1186/1471-2199-6-14 1471-2199
24. T. A. Knotts, N. Rathore, C. Schwartz, and J. J. de Pablo, J. Chem. Phys. JCPSA6 0021-9606 126, 084901 (2007). 10.1063/1.2431804
25. M. Feig and B. M. Pettitt, Biophys. J. BIOJAU 0006-3495 75, 134 (1998). 10.1016/S0006-3495(98)77501-0
26. F. Merzel, F. Fontaine-Vive, M. R. Johnson, and G. J. Kearley, Phys. Rev. E PLEEE8 1063-651X 76, 031917 (2007). 10.1103/PhysRevE.76.031917
27. C. Hyeon and D. Thirumalai, Biophys. J. BIOJAU 0006-3495 92, 731 (2007). 10.1529/biophysj.106.093062
28. F. Ding, S. Sharma, P. Chalasani, V. V. Demidov, N. E. Broude, and N. V. Dokholyan, RNA RNARFU 1355-8382 14, 1164 (2008). 10.1261/rna.894608
29. R. Das and D. Baker, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 104, 14664 (2007). 10.1073/pnas.0703836104
30. M. Parisien and F. Major, Nature (London) NATUAS 0028-0836 452, 51 (2008). 10.1038/nature06684
31. R. Das, M. Kudaravalli, M. Jonikas, A. Laederach, R. Fong, J. P. Schwans, D. Baker, J. A. Piccirilli, R. B. Altman, and D. Herschlag, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 105, 4144 (2008). 10.1073/pnas.0709032105
32. D. Poland and H. A. Scheraga, J. Chem. Phys. JCPSA6 0021-9606 45, 1456 (1966). 10.1063/1.1727785
33. J. Reeder and R. Giegerich, BMC Bioinf. BBMIC4 1471-2105 5, 104 (2004). 10.1186/1471-2105-5-104
34. R. M. Dirks and N. A. Pierce, J. Comput. Chem. JCCHDD 0192-8651 24, 1664 (2003). 10.1002/jcc.10296
35. I. Tinoco, Jr. and C. Bustamante, J. Mol. Biol. JMOBAK 0022-2836 293, 271 (1999). 10.1006/jmbi.1999.3001
36. Y. Byun and K. Han, Nucleic Acids Res. NARHAD 0305-1048 34, W416 (2006). 10.1093/nar/gkl210
37. M. J. Serra and D. H. Turner, Methods Enzymol. MENZAU 0076-6879 259, 242 (1995). 10.1016/0076-6879(95)59047-1
38. A. P. Gultyaev, F. H. van Batenburg, and C. W. Pleij, RNA RNARFU 1355-8382 5, 609 (1999). 10.1017/S135583829998189X
39. S. Cao and S. J. Chen, Nucleic Acids Res. NARHAD 0305-1048 34, 2634 (2006). 10.1093/nar/gkl346
40. P. Schuster, Rep. Prog. Phys. RPPHAG 0034-4885 69, 1419 (2006). 10.1088/0034-4885/69/5/R04
41. H. Jacobson and W. H. Stockmayer, J. Chem. Phys. JCPSA6 0021-9606 18, 1600 (1950). 10.1063/1.1747547
42. M. E. Fisher, J. Chem. Phys. JCPSA6 0021-9606 45, 1469 (1966). 10.1063/1.1727787
43. Y. Kafri, D. Mukamel, and L. Peliti, Eur. Phys. J. B EPJBFY 1434-6028 27, 135 (2002).
44. E. Carlon, E. Orlandini, and A. L. Stella, Phys. Rev. Lett. PRLTAO 0031-9007 88, 198101 (2002). 10.1103/PhysRevLett.88.198101
45. R. Blossey and E. Carlon, Phys. Rev. E PLEEE8 1063-651X 68, 061911 (2003). 10.1103/PhysRevE.68.061911
46. D. Jost and R. Everaers, J. Phys.: Condens. Matter JCOMEL 0953-8984 21, 034108 (2009). 10.1088/0953-8984/21/3/034108
47. S. Cao and S. J. Chen, RNA RNARFU 1355-8382 15, 696 (2009). 10.1261/rna.1429009
48. G. Vernizzi, H. Orland, and A. Zee, e-print arXiv:q-bio/0405014.
49. M. Bon, G. Vernizzi, H. Orland, and A. Zee, J. Mol. Biol. JMOBAK 0022-2836 379, 900 (2008). 10.1016/j.jmb.2008.04.033
50. A. Lucas and K. A. Dill, J. Chem. Phys. JCPSA6 0021-9606 119, 2414 (2003). 10.1063/1.1587129
51. Z. Kopeikin and S. J. Chen, J. Chem. Phys. JCPSA6 0021-9606 122, 094909 (2005). 10.1063/1.1857831
52. Z. Kopeikin and S. J. Chen, J. Chem. Phys. JCPSA6 0021-9606 124, 154903 (2006). 10.1063/1.2188940
53. M. S. Causo, B. Coluzzi, and P. Grassberger, Phys. Rev. E PLEEE8 1063-651X 62, 3958 (2000). 10.1103/PhysRevE.62.3958
54. P. Leoni and C. Vanderzande, Phys. Rev. E PLEEE8 1063-651X 68, 051904 (2003). 10.1103/PhysRevE.68.051904
55. A. Kabaķioǧlu and A. L. Stella, Phys. Rev. E PLEEE8 1063-651X 70, 011802 (2004). 10.1103/PhysRevE.70.011802
56. M. Sales-Pardo, R. Guimera, A. A. Moreira, J. Widom, and L. A. N. Amaral, Phys. Rev. E PLEEE8 1063-651X 71, 051902 (2005). 10.1103/PhysRevE.71.051902
57. R. Everaers, S. Kumar, and C. Simm, Phys. Rev. E PLEEE8 1063-651X 75, 041918 (2007). 10.1103/PhysRevE.75.041918
58. T. E. Ouldridge, I. G. Johnston, A. A. Louis, and J. P. K. Doye, J. Chem. Phys. JCPSA6 0021-9606 130, 065101 (2009). 10.1063/1.3055595
59. K. Takamoto, R. Das, Q. He, S. Doniach, M. Brenowitz, D. Herschlag, and M. R. Chance, J. Mol. Biol. JMOBAK 0022-2836 343, 1195 (2004). 10.1016/j.jmb.2004.08.080
60. N. Xia, J. SantaLucia, Jr. M. E. Burkard, R. Kierzek, S. J. Schroeder, X. Jiao, C. Cox, and D. H. Turner, Biochemistry BICHAW 0006-2960 37, 14719 (1998). 10.1021/bi9809425
61. D. M. Gray and I. Tinoco, Jr. Biopolymers BIPMAA 0006-3525 9, 223 (1970). 10.1002/bip.1970.360090207
62. N. B. Leontis and E. Westhof, RNA RNARFU 1355-8382 7, 499 (2001). 10.1017/S1355838201002515
63. A. Dkhissi, G. Renvez, and R. Blossey, J. Phys.: Condens. Matter JCOMEL 0953-8984 21, 034115 (2009). 10.1088/0953-8984/21/3/034115
64. P. -G. de Gennes, Scaling Concepts in Polymer Physics (Cornell University Press, Ithaca, 1979).
65. C. Vanderzande, Lattice Models of Polymers (Cambridge University Press, Cambridge, UK, 1998). 10.1017/CBO9780511563935
66. J. L. Martin, M. F. Sykes, and F. T. Hioe, J. Chem. Phys. JCPSA6 0021-9606 46, 3478 (1967). 10.1063/1.1841242
67. W. H. Press, S. A. Teukolsky, W. T. Vetterling, and B. P. Flannery, Numerical Recipes in Fortran 77: The Art of Scientific Computing (Cambridge University Press, Cambridge, England, 1996).
68. T. Ohmichi, S. -I. Nakano, D. Miyoshi, and N. Sugimoto, J. Am. Chem. Soc. JACSAT 0002-7863 124, 10367 (2002). 10.1021/ja0255406
69. A. E. Walter, D. H. Turner, J. Kim, M. H. Lyttle, P. Muller, D. H. Mathews, and M. Zuker, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 91, 9218 (1994). 10.1073/pnas.91.20.9218
70. A. E. Walter and D. H. Turner, Biochemistry BICHAW 0006-2960 33, 12715 (1994). 10.1021/bi00208a024
71. J. Kim, A. E. Walter, and D. H. Turner, Biochemistry BICHAW 0006-2960 35, 13753 (1996). 10.1021/bi960913z
72. B. M. Znosko, M. E. Burkard, S. J. Schroeder, T. R. Krugh, and D. H. Turner, Biochemistry BICHAW 0006-2960 41, 14969 (2002). 10.1021/bi020326f
73. S. J. Johnson and L. S. Beese, Cell CELLB5 0092-8674 116, 803 (2004). 10.1016/S0092-8674(04)00252-1
74. D. M. Gray, Biopolymers BIPMAA 0006-3525 42, 783 (1997). 10.1002/(SICI)1097-0282(199712)42:7<783::AID-BIP4>3.0.CO;2-P
75. D. M. Gray, Biopolymers BIPMAA 0006-3525 42, 795 (1997). 10.1002/(SICI)1097-0282(199712)42:7<795::AID-BIP5>3.0.CO;2-O
76. M. J. Serra, T. W. Barnes, K. Betschart, M. J. Gutierrez, K. J. Sprouse, C. K. Riley, L. Stewart, and R. E. Temel, Biochemistry BICHAW 0006-2960 36, 4844 (1997). 10.1021/bi962608j
77. C. W. Hilbers, C. A. G. Haasnoot, S. H. de Bruin, J. J. M. Joordens, G. A. Van Der Marel, and J. H. Van Boom, Biochimie BICMBE 0300-9084 67, 685 (1985). 10.1016/S0300-9084(85)80156-5
78. R. M. Wartell and A. S. Benight, Phys. Rep. PRPLCM 0370-1573 126, 67 (1985). 10.1016/0370-1573(85)90060-2
79. R. D. Blake and S. G. Delcourt, Nucleic Acids Res. NARHAD 0305-1048 26, 3323 (1998). 10.1093/nar/26.14.3323
80. J. SantaLucia, Jr. Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 95, 1460 (1998). 10.1073/pnas.95.4.1460
81. M. Doi and S. F. Edwards, The Theory of Polymer Dynamics (Oxford University Press, New York, 1986).
82. C. Bustamante, J. F. Marko, E. D. Siggia, and S. Smith, Science SCIEAS 0036-8075 265, 1599 (1994). 10.1126/science.8079175
83. D. Frenkel and B. Smit, Understanding Molecular Simulation: From Algorithms to Applications (Academic, San Diego, 2002).
84. N. Madras and A. D. Sokal, J. Stat. Phys. JSTPBS 0022-4715 50, 109 (1988). 10.1007/BF01022990
85. N. Madras, A. Orlitsky, and L. A. Shepp, J. Stat. Phys. JSTPBS 0022-4715 58, 159 (1990). 10.1007/BF01020290
86. A. D. Sokal, e-print arXiv:hep-lat/9509032.
87. N. Metropolis, A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller, and E. Teller, J. Chem. Phys. JCPSA6 0021-9606 21, 1087 (1953). 10.1063/1.1699114
88. E. J. Janse van Rensburg, S. G. Whittington, and N. Madras, J. Phys. A JPHAC5 0305-4470 23, 1589 (1990). 10.1088/0305-4470/23/9/021
89. A. M. Ferrenberg and R. H. Swendsen, Phys. Rev. Lett. PRLTAO 0031-9007 63, 1195 (1989). 10.1103/PhysRevLett.63.1195
90. G. Varani, Annu. Rev. Biophys. Biomol. Struct. ABBSE4 1056-8700 24, 379 (1995). 10.1146/annurev.bb.24.060195.002115
91. M. A. Glucksmann-Kuis, X. Dai, P. Markiewicz, and L. B. Rothman-Denes, Cell CELLB5 0092-8674 84, 147 (1996). 10.1016/S0092-8674(00)81001-6
92. H. Lodish, A. Berk, S. L. Zipursky, P. Matsudaira, D. Baltimore, and J. E. Darnell, Molecular Cell Biology (W. H. Freeman and Company, New York, 2000).
93. O. C. Uhlenbeck, Nature (London) NATUAS 0028-0836 346, 613 (1990). 10.1038/346613a0
94. J. Liphardt, B. Onoa, S. B. Smith, I. Tinoco, Jr. and C. Bustamante, Science SCIEAS 0036-8075 292, 733 (2001). 10.1126/science.1058498
95. D. Collin, F. Ritort, C. Jarzynski, S. B. Smith, I. Tinoco, Jr. and C. Bustamante, Nature (London) NATUAS 0028-0836 437, 231 (2005). 10.1038/nature04061
96. A. Ke, K. Zhou, F. Ding, J. H. Cate, and J. A. Doudna, Nature (London) NATUAS 0028-0836 429, 201 (2004). 10.1038/nature02522
97. P. L. Adams, M. R. Stahley, A. B. Kosek, J. Wang, and S. A. Strobel, Nature (London) NATUAS 0028-0836 430, 45 (2004). 10.1038/nature02642
98. C. A. Theimer, C. A. Blois, and J. Feigon, Mol. Cell MOCEFL 1097-2765 17, 671 (2005). 10.1016/j.molcel.2005.01.017
99. L. X. Shen and I. Tinoco, Jr. J. Mol. Biol. JMOBAK 0022-2836 247, 963 (1995). 10.1006/jmbi.1995.0193
100. D. W. Staple and S. E. Butcher, PLoS Biol. PBLIBG 1545-7885 3, e213 (2005). 10.1371/journal.pbio.0030213
101. C. A. Theimer and D. P. Giedroc, J. Mol. Biol. JMOBAK 0022-2836 289, 1283 (1999). 10.1006/jmbi.1999.2850
102. S. Cao and S. -J. Chen, Phys. Biol. PBHIAT 1478-3975 5, 016002 (2008). 10.1088/1478-3975/5/1/016002
103. F. H. van Batenburg, A. P. Gultyaev, and C. W. Pleij, Nucleic Acids Res. NARHAD 0305-1048 28, 201 (2000). 10.1093/nar/28.1.201
104. V. K. Misra, R. Shiman, and D. E. Draper, Biopolymers BIPMAA 0006-3525 69, 118 (2003). 10.1002/bip.10353
105. D. Thirumalai and C. Hyeon, Biochemistry BICHAW 0006-2960 44, 4957 (2005). 10.1021/bi047314+
106. D. E. Draper, RNA RNARFU 1355-8382 10, 335 (2004). 10.1261/rna.5205404
107. J. H. Cate, A. R. Gooding, E. Podell, K. Zhou, B. L. Golden, C. E. Kundrot, T. R. Cech, and J. A. Doudna, Science SCIEAS 0036-8075 273, 1678 (1996). 10.1126/science.273.5282.1678
108. F. L. Murphy and T. R. Cech, Biochemistry BICHAW 0006-2960 32, 5291 (1993). 10.1021/bi00071a003
109. A. M. Yoffe, P. Prinsen, A. Gopal, C. M. Knobler, W. M. Gelbart, and A. Ben-Shaul, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 105, 16153 (2008). 10.1073/pnas.0808089105