Display options
Cite
Cao S, Chen SJ. Statistical mechanical modeling of RNA folding: from free energy landscape to tertiary structural prediction. Nucleic Acids Mol Biol. 2012;27:185-212doi: 10.1007/978-3-642-25740-7_10.
Cao, S., & Chen, S. J. (2012). Statistical mechanical modeling of RNA folding: from free energy landscape to tertiary structural prediction. Nucleic acids and molecular biology, 27185-212. https://doi.org/10.1007/978-3-642-25740-7_10
Cao, Song, and Chen, Shi-Jie. "Statistical mechanical modeling of RNA folding: from free energy landscape to tertiary structural prediction." Nucleic acids and molecular biology vol. 27 (2012): 185-212. doi: https://doi.org/10.1007/978-3-642-25740-7_10
Cao S, Chen SJ. Statistical mechanical modeling of RNA folding: from free energy landscape to tertiary structural prediction. Nucleic Acids Mol Biol. 2012;27:185-212. doi: 10.1007/978-3-642-25740-7_10. Epub 2012 Apr 07. PMID: 27293312; PMCID: PMC4902161.
Copy Download .nbib Format: NLM
Share it on

Nucleic Acids Mol Biol. 2012;27:185-212. doi: 10.1007/978-3-642-25740-7_10. Epub 2012 Apr 07.

Statistical mechanical modeling of RNA folding: from free energy landscape to tertiary structural prediction.

Nucleic acids and molecular biology

Song Cao, Shi-Jie Chen

Affiliations

  1. Department of Physics and Department of Biochemistry, University of Missouri, Columbia, MO 65211.

PMID: 27293312 PMCID: PMC4902161 DOI: 10.1007/978-3-642-25740-7_10

Abstract

In spite of the success of computational methods for predicting RNA secondary structure, the problem of predicting RNA tertiary structure folding remains. Low-resolution structural models show promise as they allow for rigorous statistical mechanical computation for the conformational entropies, free energies, and the coarse-grained structures of tertiary folds. Molecular dynamics refinement of coarse-grained structures leads to all-atom 3D structures. Modeling based on statistical mechanics principles also has the unique advantage of predicting the full free energy landscape, including local minima and the global free energy minimum. The energy landscapes combined with the 3D structures form the basis for quantitative predictions of RNA functions. In this chapter, we present an overview of statistical mechanical models for RNA folding and then focus on a recently developed RNA statistical mechanical model -- the

References

  1. Biophys J. 2004 Jul;87(1):215-26 - PubMed
  2. Annu Rev Biophys. 2008;37:197-214 - PubMed
  3. Nucleic Acids Res. 2006 May 18;34(9):2634-52 - PubMed
  4. RNA. 2007 Jul;13(7):939-51 - PubMed
  5. J Mol Biol. 2002 Jun 21;319(5):1059-66 - PubMed
  6. Biochemistry. 1999 Mar 23;38(12):3468-77 - PubMed
  7. BMC Bioinformatics. 2004 Aug 04;5:104 - PubMed
  8. Science. 1996 Feb 9;271(5250):795-9 - PubMed
  9. Bioinformatics. 2006 May 15;22(10):1177-82 - PubMed
  10. Nat Struct Biol. 1999 Mar;6(3):285-92 - PubMed
  11. J Mol Biol. 1998 Dec 18;284(5):1465-78 - PubMed
  12. RNA. 2008 Jun;14(6):1164-73 - PubMed
  13. Curr Opin Struct Biol. 2006 Jun;16(3):307-18 - PubMed
  14. Science. 2000 Aug 11;289(5481):905-20 - PubMed
  15. RNA. 2010 Mar;16(3):538-52 - PubMed
  16. Bioinformatics. 2005 Aug 1;21(15):3320-1 - PubMed
  17. J Mol Biol. 2000 Apr 28;298(2):167-85 - PubMed
  18. RNA. 1999 Nov;5(11):1458-69 - PubMed
  19. Proc Natl Acad Sci U S A. 2005 Jun 7;102(23):8080-5; discussion 8077-9 - PubMed
  20. Bioinformatics. 2006 Jul 15;22(14):e90-8 - PubMed
  21. Nucleic Acids Res. 2003 Aug 15;31(16):4755-61 - PubMed
  22. RNA. 2001 Apr;7(4):499-512 - PubMed
  23. Biophys J. 2006 Feb 15;90(4):1175-90 - PubMed
  24. J Mol Biol. 2007 Mar 30;367(3):909-24 - PubMed
  25. Phys Biol. 2008 Mar 11;5(1):016002 - PubMed
  26. F1000 Biol Rep. 2010 Jan 27;2:8 - PubMed
  27. Bioinformatics. 2009 Oct 15;25(20):2646-54 - PubMed
  28. Science. 2001 Apr 27;292(5517):733-7 - PubMed
  29. RNA. 2008 Mar;14(3):465-81 - PubMed
  30. Proc Natl Acad Sci U S A. 1999 Dec 7;96(25):14234-9 - PubMed
  31. Curr Opin Struct Biol. 2009 Jun;19(3):267-76 - PubMed
  32. Trends Biotechnol. 1998 Apr;16(4):190-6 - PubMed
  33. PLoS Biol. 2005 Jun;3(6):e213 - PubMed
  34. Cell. 2001 Jul 27;106(2):233-41 - PubMed
  35. RNA. 2009 Apr;15(4):696-706 - PubMed
  36. Proc Natl Acad Sci U S A. 1980 Nov;77(11):6309-13 - PubMed
  37. Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12694-9 - PubMed
  38. Nat Struct Mol Biol. 2009 Mar;16(3):343-4 - PubMed
  39. J Mol Biol. 1998 Jun 19;279(4):773-93 - PubMed
  40. RNA. 2008 Dec;14(12):2465-77 - PubMed
  41. RNA. 2003 Feb;9(2):168-74 - PubMed
  42. Comput Appl Biosci. 1997 Aug;13(4):459-71 - PubMed
  43. RNA. 2006 Mar;12(3):323-31 - PubMed
  44. Nature. 2000 Sep 21;407(6802):327-39 - PubMed
  45. Prog Biophys Mol Biol. 2000;74(1-2):115-40 - PubMed
  46. J Mol Biol. 2005 Nov 11;353(5):1199-209 - PubMed
  47. Mol Cell Biol. 2007 Mar;27(6):2130-43 - PubMed
  48. Biochem Biophys Res Commun. 1972 Sep 26;48(6):1392-9 - PubMed
  49. Proc Natl Acad Sci U S A. 2009 Aug 4;106(31):12706-11 - PubMed
  50. Proc Natl Acad Sci U S A. 2007 Sep 11;104(37):14664-9 - PubMed
  51. Nature. 2008 Mar 6;452(7183):51-5 - PubMed
  52. Cell Mol Life Sci. 2000 May;57(5):796-808 - PubMed
  53. Science. 1996 Sep 20;273(5282):1678-85 - PubMed
  54. J Mol Biol. 2008 Jan 11;375(2):572-80 - PubMed
  55. Nucleic Acids Res. 2002 Dec 1;30(23):5094-102 - PubMed
  56. Nat Genet. 2007 Oct;39(10):1278-84 - PubMed
  57. RNA. 2004 Oct;10(10):1507-17 - PubMed
  58. Science. 1994 Aug 12;265(5174):918-24 - PubMed
  59. Proc Natl Acad Sci U S A. 2002 Jan 8;99(1):155-60 - PubMed
  60. Mol Cell. 2005 Mar 4;17(5):671-82 - PubMed
  61. Annu Rev Biochem. 1996;65:741-68 - PubMed
  62. J Am Chem Soc. 2009 Feb 25;131(7):2541-6 - PubMed
  63. Nucleic Acids Res. 2010 Apr;38(7):e103 - PubMed
  64. J Mol Graph Model. 2006 Oct;25(2):261-74 - PubMed
  65. J Mol Biol. 2006 Mar 17;357(1):292-312 - PubMed
  66. J Mol Biol. 1995 Jun 30;250(1):37-51 - PubMed
  67. Proc Natl Acad Sci U S A. 2005 May 10;102(19):6789-94 - PubMed
  68. J Mol Biol. 2005 Feb 4;345(5):987-1001 - PubMed
  69. Nat Struct Mol Biol. 2007 Apr;14(4):287-94 - PubMed
  70. Biopolymers. 1972 Jan;11(1):1-23 - PubMed
  71. J Mol Biol. 2003 Aug 15;331(3):571-83 - PubMed
  72. J Mol Biol. 1999 Feb 5;285(5):2053-68 - PubMed
  73. Bioinformatics. 2004 Jan 1;20(1):58-66 - PubMed
  74. Virus Res. 2009 Feb;139(2):193-208 - PubMed
  75. Proc Natl Acad Sci U S A. 2000 Jun 6;97(12):6515-20 - PubMed
  76. Nucleic Acids Res. 2003 Jul 1;31(13):3429-31 - PubMed
  77. Biopolymers. 1990 May-Jun;29(6-7):1105-19 - PubMed
  78. J Comput Chem. 2005 Dec;26(16):1668-88 - PubMed
  79. RNA. 2009 Feb;15(2):189-99 - PubMed
  80. Curr Opin Struct Biol. 2007 Apr;17(2):157-65 - PubMed
  81. J Mol Biol. 1998 Jul 24;280(4):597-609 - PubMed
  82. Science. 1989 Apr 7;244(4900):48-52 - PubMed
  83. Curr Opin Biotechnol. 1997 Feb;8(1):36-44 - PubMed
  84. J Biol Chem. 2009 Apr 24;284(17):11012-6 - PubMed
  85. Methods. 2009 Oct;49(2):189-96 - PubMed
  86. Proc Natl Acad Sci U S A. 2000 Jan 18;97(2):646-51 - PubMed
  87. Science. 2001 May 4;292(5518):883-96 - PubMed
  88. J Comput Biol. 2006 Mar;13(2):267-82 - PubMed
  89. J Comput Chem. 2003 Oct;24(13):1664-77 - PubMed
  90. RNA. 2010 Jan;16(1):26-42 - PubMed
  91. Curr Opin Cell Biol. 1990 Dec;2(6):1099-103 - PubMed
  92. J Mol Biol. 2002 Mar 22;317(2):191-203 - PubMed
  93. Mol Cell. 2009 Mar 27;33(6):784-90 - PubMed
  94. J Mol Biol. 1999 May 7;288(3):305-20 - PubMed
  95. RNA. 2005 Dec;11(12):1884-97 - PubMed
  96. J Chem Theory Comput. 2006 May 1;2(3):529-540 - PubMed
  97. Nucleic Acids Res. 2003 Dec 15;31(24):7280-301 - PubMed
  98. Proc Natl Acad Sci U S A. 1993 Oct 15;90(20):9408-12 - PubMed
  99. Phys Biol. 2004 Jun;1(1-2):19-26 - PubMed
  100. Nat Rev Microbiol. 2007 Aug;5(8):598-610 - PubMed
  101. Nucleic Acids Res. 2005 Apr 14;33(7):2210-4 - PubMed
  102. Proc Natl Acad Sci U S A. 2007 Apr 24;104(17):7045-50 - PubMed
  103. J Mol Biol. 2008 Dec 31;384(5):1249-61 - PubMed
  104. J Chem Phys. 1966 Sep 1;45(5):1464-9 - PubMed
  105. Nat Struct Mol Biol. 2008 Jun;15(6):634-40 - PubMed
  106. RNA. 2005 Oct;11(10):1494-504 - PubMed
  107. Proc Natl Acad Sci U S A. 2009 Jan 6;106(1):97-102 - PubMed
  108. Cell. 1998 Feb 6;92(3):315-26 - PubMed
  109. Proc Natl Acad Sci U S A. 2008 Mar 18;105(11):4144-9 - PubMed
  110. Prog Nucleic Acid Res Mol Biol. 1991;41:131-77 - PubMed
  111. J Mol Biol. 2000 Feb 18;296(2):659-71 - PubMed
  112. Nature. 2006 May 11;441(7090):244-7 - PubMed
  113. J Chem Phys. 2008 Mar 28;128(12):125107 - PubMed
  114. RNA. 2009 Dec;15(12):2248-63 - PubMed
  115. Biopolymers. 1997;44(3):309-19 - PubMed
  116. Cell. 2009 Feb 20;136(4):577-80 - PubMed
  117. Cell. 2009 Jan 23;136(2):215-33 - PubMed
  118. Nucleic Acids Res. 1986 Jan 10;14(1):299-315 - PubMed
  119. Macromolecules. 1975 May-Jun;8(3):272-5 - PubMed
  120. J Mol Biol. 1991 Aug 20;220(4):889-902 - PubMed
  121. Biochem Soc Trans. 2008 Aug;36(Pt 4):684-9 - PubMed
  122. Proc Natl Acad Sci U S A. 2007 Apr 3;104(14):5830-5 - PubMed
  123. Nucleic Acids Res. 1987 Nov 25;15(22):9109-28 - PubMed
  124. Proc Natl Acad Sci U S A. 2001 Apr 24;98(9):4899-903 - PubMed
  125. J Phys Chem B. 2011 Apr 14;115(14):4216-26 - PubMed
  126. J Mol Biol. 1999 May 21;288(5):911-40 - PubMed
  127. Nucleic Acids Res. 2006;34(17):4912-24 - PubMed
  128. J Mol Biol. 2002 Sep 20;322(3):621-33 - PubMed
  129. Methods Enzymol. 1995;259:242-61 - PubMed
  130. Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16998-7003 - PubMed
  131. Proc Natl Acad Sci U S A. 1998 Feb 17;95(4):1460-5 - PubMed
  132. RNA. 1999 May;5(5):609-17 - PubMed
  133. Nucleic Acids Res. 2003 Jul 1;31(13):3406-15 - PubMed
  134. Bioinformatics. 2009 Jun 15;25(12):i365-73 - PubMed
  135. Nature. 2009 Aug 6;460(7256):711-6 - PubMed
  136. Nucleic Acids Res. 2007;35(18):6150-60 - PubMed

Publication Types

Grant support