Kinetic Monte Carlo approach to RNA folding dynamics using structure-based models

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Volumn 88, Issue 5, 2013, Pages

  Faber, Michael ^a   Klumpp, Stefan ^a  

^a MAX PLANCK INSTITUTE OF COLLOIDS AND INTERFACES   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMICAL ACTIVITY; COMPLEX STRUCTURE; FOLDING DYNAMICS; KINETIC MONTE CARLO; KINETIC MONTE CARLO SIMULATION; RNA SECONDARY STRUCTURES; STRONG CORRELATION; THREE-DIMENSIONAL STRUCTURE;

CONDENSED MATTER PHYSICS; PHYSICS;

RNA;

TRANSFER RNA;

ARTICLE; BASE PAIRING; CHEMICAL STRUCTURE; CHEMISTRY; GENETICS; INVERTED REPEAT; KINETICS; MONTE CARLO METHOD; RNA FOLDING;

BASE PAIRING; INVERTED REPEAT SEQUENCES; KINETICS; MODELS, MOLECULAR; MONTE CARLO METHOD; RNA FOLDING; RNA, TRANSFER;

EID: 84888246108     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.88.052701     Document Type: Article

References (45)

1. M. J. Fedor and J. R. Williamson, Nat. Rev. Mol. Cell Biol. NRMCBP 1471-0072 10.1038/nrm1647 6, 399 (2005). (Pubitemid 40637857)
2. L. S. Waters and G. Storz, Cell CELLB5 0092-8674 10.1016/j.cell.2009.01. 043 136, 615 (2009).
3. M. Mandal and R. R. Breaker, Nat. Rev. Mol. Cell Biol. NRMCBP 1471-0072 10.1038/nrm1403 5, 451 (2004). (Pubitemid 38745495)
4. T. R. Cech, Science SCIEAS 0036-8075 10.1126/science.289.5481.878 289, 878 (2000). (Pubitemid 30659934)
5. I. Tinoco, Jr. and C. Bustamante, J. Mol. Biol. JMOBAK 0022-2836 10.1006/jmbi.1999.3001 293, 271 (1999). (Pubitemid 29516169)
6. K. A. Dill, S. B. Ozkan, M. S. Shell, and T. R. Weikl, Annu. Rev. Biophys. 1936-122X 10.1146/annurev.biophys.37.092707.153558 37, 289 (2008).
7. I. Hofacker, W. Fontana, P. Stadler, L. Bonhoeffer, M. Tacker, and P. Schuster, Monatshefte für Chemie/Chemical Monthly 0026-9247 10.1007/BF00818163 125, 167 (1994).
8. J. R. Vieregg and I. Tinoco, Mol. Phys. MOPHAM 0026-8976 10.1080/00268970500525986 104, 1343 (2006).
9. E. J. Sorin, B. J. Nakatani, Y. M. Rhee, G. Jayachandran, V. Vishal, and V. S. Pande, J. Mol. Biol. JMOBAK 0022-2836 10.1016/j.jmb.2004.02.024 337, 789 (2004). (Pubitemid 38368925)
10. C. Flamm, W. Fontana, I. L. Hofacker, and P. Schuster, RNA 1355-8382 10.1017/S1355838200992161 6, 325 (2000). (Pubitemid 30161278)
11. H. Isambert and E. D. Siggia, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.110533697 97, 6515 (2000). (Pubitemid 30412745)
12. D. Pörschke, Biophys. Chem. BICIAZ 0301-4622 10.1016/0301-4622(74) 85008-8 1, 381 (1974).
13. B. Sauerwine and M. Widom, Phys. Rev. E PLEEE8 1539-3755 10.1103/PhysRevE.84.061912 84, 061912 (2011).
14. P. C. Whitford, A. Schug, J. Saunders, S. P. Hennelly, J. N. Onuchic, and K. Y. Sanbonmatsu, Biophys. J. BIOJAU 0006-3495 10.1016/j.bpj.2008.10.033 96, L7 (2009).
15. M. Zacharias, Curr. Opin. Struct. Biol. COSBEF 0959-440X 10.1016/S0959-440X(00)00089-0 10, 311 (2000). (Pubitemid 30333100)
16. D. H. Turner and D. H. Mathews, Nucleic Acids Res. NARHAD 0305-1048 10.1093/nar/gkp892 38, D280 (2010).
17. M. Manosas, J.-D. Wen, P. T. X. Li, S. B. Smith, C. Bustamante, I. Tinoco, Jr., and F. Ritort, Biophys. J. BIOJAU 0006-3495 10.1529/biophysj.106. 094243 92, 3010 (2007). (Pubitemid 46684562)
18. J. N. Onuchic, Z. Luthey-Schulten, and P. G. Wolynes, Annu. Rev. Phys. Chem. ARPLAP 0066-426X 10.1146/annurev.physchem.48.1.545 48, 545 (1997).
19. H. S. Chan and K. A. Dill, Proteins 18PLAF 0887-3585 10.1002/(SICI)1097- 0134(19980101)30:1<2::AID-PROT2>3.0.CO;2-R 30, 2 (1998). (Pubitemid 28036107)
20. R. Bundschuh and T. Hwa, Phys. Rev. E 1063-651X 10.1103/PhysRevE.65. 031903 65, 031903 (2002). (Pubitemid 40619147)
21. P. G. Higgs, Q. Rev. Biophys. QURBAW 0033-5835 10.1017/S0033583500003620 33, 199 (2000). (Pubitemid 32059803)
22. C. Hyeon and D. Thirumalai, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.0408314102 102, 6789 (2005). (Pubitemid 40675394)
23. R. Behrouzi, J. H. Roh, D. Kilburn, R. M. Briber, and S. A. Woodson, Cell CELLB5 0092-8674 10.1016/j.cell.2012.01.057 149, 348 (2012).
24. E. A. Schultes, A. Spasic, U. Mohanty, and D. P. Bartel, Nat. Struct. Mol. Biol. 1545-9993 10.1038/nsmb1014 12, 1130 (2005). (Pubitemid 41746785)
25. J. Liphardt, B. Onoa, S. B. Smith, I. Tinoco, Jr., and C. Bustamante, Science SCIEAS 0036-8075 10.1126/science.1058498 292, 733 (2001). (Pubitemid 32385545)
26. D. H. Mathews, J. Sabina, M. Zuker, and D. H. Turner, J. Mol. Biol. JMOBAK 0022-2836 10.1006/jmbi.1999.2700 288, 911 (1999). (Pubitemid 29248642)
27. P. Brion and E. Westhof, Annu. Rev. Biophys. Biomol. Struct. ABBSE4 1056-8700 10.1146/annurev.biophys.26.1.113 26, 113 (1997). (Pubitemid 27255369)
28. M. Zuker, Nucleic Acids Res. 1362-4962 10.1093/nar/gkg595 31, 3406 (2003). (Pubitemid 37442169)
29. S. Cocco, J. F. Marko, and R. Monasson, Eur. Phys. J. E EPJSFH 1292-8941 10.1140/epje/e2003-00019-8 10, 153 (2003).
30. N. Metropolis, A. Rosenbluth, M. Rosenbluth, A. Teller, and E. Teller, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1699114 21, 1087 (1953).
31. M. Faber and S. Klumpp, in From Computational Biophysics to Systems Biology (CBSB11), edited by, P. Carloni, U. H. E. Hansmann, T. Lippert, J. H. Meinke, S. Mohanty, W. Nadler, and, O. Zimmermann, (Forschungszentrum Jülich GmbH, Germany, 2012), p. 45.
32. D. R. Groebe and O. C. Uhlenbeck, Nucleic Acids Res. NARHAD 0305-1048 10.1093/nar/16.24.11725 16, 11725 (1988).
33. D. M. Crothers, P. E. Cole, C. W. Hilbers, and R. G. Shulman, J. Mol. Biol. JMOBAK 0022-2836 10.1016/0022-2836(74)90560-9 87, 63 (1974).
34. J.-D. Wen, M. Manosas, P. X. Li, S. B. Smith, C. Bustamante, F. Ritort, and I. Tinoco, Jr., Biophys. J. BIOJAU 0006-3495 10.1529/biophysj.106.094052 92, 2996 (2007). (Pubitemid 46684561)
35. C. Bustamante, J. F. Marko, E. D. Siggia, and S. Smith, Science SCIEAS 0036-8075 10.1126/science.8079175 265, 1599 (1994).
36. G. Caliskan, C. Hyeon, U. Perez-Salas, R. M. Briber, S. A. Woodson, and D. Thirumalai, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.95.268303 95, 268303 (2005). (Pubitemid 43061592)
37. C. Hyeon and D. Thirumalai, Biophys. J. BIOJAU 0006-3495 10.1016/j.bpj.2012.01.003 102, L11 (2012).
38. M. E. Craig, D. M. Crothers, and P. Doty, J. Mol. Biol. JMOBAK 0022-2836 10.1016/0022-2836(71)90434-7 62, 383 (1971).
39. H. Bhaskaran, A. Rodriguez-Hernandez, and J. J. Perona, RNA 1355-8382 10.1261/rna.030080.111 18, 569 (2012).
40. D. J. Proctor, H. Ma, E. Kierzek, R. Kierzek, M. Gruebele, and P. C. Bevilacqua, Biochemistry 0006-2960 10.1021/bi048213e 43, 14004 (2004). (Pubitemid 39482750)
41. D. Riesner and R. Romer, in Physico-chemical Properties of Nucleic Acids, edited by, J. Duchesne, (Academic Press, New York, 1973), Vol. 2, p. 237.
42. V. Serebrov, R. J. Clarke, H. J. Gross, and L. Kisselev, Biochemistry 0006-2960 10.1021/bi002241p 40, 6688 (2001). (Pubitemid 32552793)
43. S. V. Kuznetsov, C. C. Ren, S. A. Woodson, and A. Ansari, Nucleic Acids Res. NARHAD 0305-1048 10.1093/nar/gkm1083 36, 1098 (2008). (Pubitemid 351330928)
44. M. L. Deras, M. Brenowitz, C. Y. Ralston, M. R. Chance, and S. A. Woodson, Biochemistry 0006-2960 10.1021/bi0010118 39, 10975 (2000).
45. T. Xia, J. SantaLucia, Jr., M. E. Burkard, R. Kierzek, S. J. Schroeder, X. Jiao, C. Cox, and D. H. Turner, Biochemistry 0006-2960 10.1021/bi9809425 37, 14719 (1998). (Pubitemid 28487580)