Ab initio RNA folding

Journal of Physics Condensed Matter

Volumn 27, Issue 23, 2015, Pages

  Cragnolini, Tristan ^a,c   Derreumaux, Philippe ^a,b   Pasquali, Samuela ^a  

^a CNRS   (France)

^b INSTITUT UNIVERSITAIRE DE FRANCE   (France)

^c UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

coarse grained models; force field; RNA

Indexed keywords

CRYSTALLOGRAPHY; DATA MINING; FORECASTING; MOBILE SECURITY; RNA; X RAY CRYSTALLOGRAPHY;

COARSE GRAINED MODELS; EQUILIBRIUM STRUCTURES; EXPERIMENTAL DETERMINATION; FORCE FIELDS; PHENOMENOLOGICAL MODELS; SECONDARY STRUCTURE PREDICTION; THEORETICAL APPROACH; THREE-DIMENSIONAL STRUCTURE;

BIOINFORMATICS;

RNA;

BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; RNA FOLDING;

COMPUTATIONAL BIOLOGY; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; RNA; RNA FOLDING;

EID: 84930226610     PISSN: 09538984     EISSN: 1361648X     Source Type: Journal    
DOI: 10.1088/0953-8984/27/23/233102     Document Type: Review

References (144)

1. Ban N, Nissen P, Hansen J, Moore P B and Steitz T A 2000 The complete atomic structure of the large ribosomal subunit at 2.4 A resolution Science 289 905-20
2. Nissen P, Hansen J, Ban N, Moore P B and Steitz T A 2000 The structural basis of ribosome activity in peptide bond synthesis Science 289 920-30
3. Toor N, Keating K S, Taylor S D and Pyle A M 2008 Crystal structure of a self-spliced group II intron Science 320 77-82
4. Ferré-D'Amaré A R 2010 The glmS ribozyme: use of a small molecule coenzyme by a gene-regulatory RNA Q. Rev. Biophys. 43 423-47
5. Grabow W W, Zakrevsky P, Afonin K A, Chworos A, Shapiro B A and Jaeger L 2011 Self-assembling RNA nanorings based on RNAI/II inverse kissing complexes Nano Lett. 11 878-87
6. Hao C, Li X, Tian C, Jiang W, Wang G and Mao C 2014 Construction of RNA nanocages by re-engineering the packaging RNA of Phi29 bacteriophage Nat. commun. 5 3890
7. Afonin K A, Bindewald E, Yaghoubian A J, Voss N, Jacovetty E, Shapiro B a and Jaeger L 2010 In vitro assembly of cubic RNA-based scaffolds designed in silico Nat. Nanotechnol. 5 676-82
8. Khisamutdinov E F, Jasinski D L and Guo P 2014 RNA as a boiling-resistant anionic polymer material to build robust structures with defined shape and stoichiometry ACS Nano 8 4771-81
9. Jaeger L and Chworos A 2006 The architectonics of programmable RNA and DNA nanostructures Curr. Opin. Struct. Biol. 16 531-43
10. Obermayer B, Krammer H, Braun D and Gerland U 2011 Emergence of information transmission in a prebiotic RNA reactor Phys. Rev. Lett. 107 018101
11. Holbrook S R 2005 RNA structure: the long and the short of it Curr. Opin. Struct. Biol. 15 302-308
12. Strobel E, Seeling K and Tebbe C C 2008 Diversity responses of rumen microbial communities to Fusarium-contaminated feed, evaluated with rumen simulating technology Environ. Microbiol. 10 483-96
13. Scott W G 2007 Ribozymes Curr. Opin. Struc. Biol. 17 280-6
14. Birney E et al 2007 Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project Nature 447 799-816
15. Leontis N B, Stombaugh J and Westhof E 2002 The non-Watson-Crick base pairs and their associated isostericity matrices Nucl. Acids Res. 30 3497-531
16. Zuker M 2000 Calculating nucleic acid secondary structure Curr. Opin. Struct. Biol. 10 303-10
17. Chastain M and Tinoco I Jr 1991 Structural elements in RNA Prog. Nucl. Acid Res. Mol. Biol. 41 131-77
18. Tinoco I Jr and Bustamante C 1999 How RNA folds J. Mol. Biol. 293 271-81
19. Reiter N J, Chan C W and Mondragón A 2011 Emerging structural themes in large RNA molecules Curr. Opin. Struct. Biol. 21 319-26
20. Onoa B, Tinoco I and Tinoco I Jr 2004 RNA folding and unfolding Curr. Opin. Struct. Biol. 14 374-9
21. Li P P T X, Vieregg J, Tinoco I Jr and Tinoco I 2008 How RNA unfolds and refolds Ann. Rev. Biochem. 77 77-100
22. Gluick T C and Draper D E 1994 Thermodynamics of folding a pseudoknotted mRNA fragment J. Mol. Biol. 241 246-62
23. Al-Hashimi H M and Walter N G 2008 RNA dynamics: it is about time Curr. Opin. Struct. Biol. 18 321-9
24. Serganov A 2009 The long and the short of riboswitches Curr. Opin. Struct. Biol. 19 251-9
25. Furtig B et al 2007 Conformational dynamics of bistable RNAs studied by time-resolved NMR spectroscopy J. Am. Chem. Soc. 129 16222-9
26. Pan J, Thirumalai D and Woodson S A 1997 Folding of RNA involves parallel pathways J. Mol. Biol. 273 7-13
27. Chen A A and García A E 2013 High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations Proc. Natl Acad. Sci. USA 110 16820-5
28. Sorin E J, Nakatani B J, Rhee Y M, Jayachandran G, Vishal V and Pande V S 2004 Does native state topology determine the RNA folding mechanism? J. Mol. Biol. 337 789-97
29. Gan H H, Pasquali S and Schlick June T 2003 Exploring the repertoire of RNA secondary motifs using graph theory; implications for RNA design Nucl. Acids Res. 31 2926-43
30. Sponer J, Riley K E and Hobza P 2008 Nature and magnitude of aromatic stacking of nucleic acid bases Phys. Chem. Chem. Phys. 10 2595-610
31. Cheatham T E and Case D A 2013 Twenty-five years of nucleic acid simulations Biopolymers 99 969-77
32. Rother K, Rother M, Boniecki M, Puton T and Bujnicki J M 2011 RNA and protein 3D structure modeling: similarities and differences J. Mol. Model. 17 2325-36
33. Rother M, Rother K, Puton T, Bujnicki J M and Bujnicki J M 2011 ModeRNA: a tool for comparative modeling of RNA 3D structure Nucl. Acids Res. 39 4007-22
34. Flores S C and Altman R B 2010 Turning limited experimental information into 3D models of RNA RNA 16 1769-78
35. Das R and Baker D 2007 Automated de novo prediction of native-like RNA tertiary structures Proc. Natl Acad. Sci. USA 104 14664-9
36. Parisien M and Major F 2008 The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data Nature 452 51-5
37. Cao S and Chen S-J 2011 Physics-based de novo prediction of RNA 3D structures J. Phys. Chem. B 115 4216-26
38. Xia Z, Gardner D P, Gutell R R and Ren P 2010 Coarse-grained model for simulation of RNA three-dimensional structures J. Phys. Chem. B 114 13497-506
39. Šulc P, Romano F, Ouldridge T E, Doye J P K and Louis A a 2014 A nucleotide-level coarse-grained model of RNA J. Chem. Phys. 140 235102
40. Cragnolini T, Laurin Y, Derreumaux P and Pasquali S 2015 The coarse-grained HiRE-RNA model for de novo calculations of RNA free energy surfaces, folding pathways and complex structure prediction arXiv: 1404.0568 [q-bio.BM]
41. Beveridge D L et al 2004 Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps Biophys. J. 87 3799-813
42. Dixit S B et al 2005 Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II: sequence context effects on the dynamical structures of the 10 unique dinucleotide steps Biophys. J. 89 3721-40
43. Joung I S and Cheatham T E 2008 Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations J. Phys. Chem. B 112 9020-41
44. Hashem Y and Auffinger P 2009 A short guide for molecular dynamics simulations of RNA systems Methods 47 187-97
45. Stadlbauer P, Krepl M, Cheatham T, Koca J and Sponer J 2013 Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations Nucl. Acids. Res. 41 7128-43
46. Kührová P, Banáš P, Best R B, Šponer J and Otyepka M 2013 Computer folding of RNA tetraloops? Are we there yet? J. Chem. Theory Comput. 9 2115-25
47. Garcia A E and Paschek D 2008 Simulation of the pressure and temperature folding/unfolding equilibrium of a small RNA hairpin J. Am. Chem. Soc. 130 815-7
48. Kannan S and Zacharias M 2007 Folding of a DNA hairpin loop structure in explicit solvent using replica-exchange molecular dynamics simulations Biophys. J. 93 3218-28
49. Chakraborty D, Collepardo-Guevara R and Wales D J 2014 Energy landscapes, folding mechanisms, and kinetics of RNA tetraloop hairpins J. Am. Chem. Soc. 136 18052-61
50. Neidle S 2010 Human telomeric G-quadruplex: the current status of telomeric G-quadruplexes as therapeutic targets in human cancer FEBS J. 277 1118-25
51. Das R, Karanicolas J and Baker D 2010 Atomic accuracy in predicting and designing noncanonical RNA structure Nat. Methods 7 291-4
52. Sorin E J, Rhee Y M and Pande V S 2005 Does water play a structural role in the folding of small nucleic acids? Biophys. J. 88 2516-24
53. Cruz J A et al 2012 RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction RNA 18 610-25
54. Laing C and Schlick T 2010 Computational approaches to 3D modeling of RNA J. Phys.: Condens. Matter 22 283101
55. Laing C and Schlick T 2011 Computational approaches to RNA structure prediction, analysis, and design Curr. Opin. Struct. Biol. 21 1-13
56. Cao S and Chen S-J 2012 A domain-based model for predicting large and complex pseudoknotted structures RNA Biol. 9 200-11
57. Shi Y-Z, Wu Y-Y, Wang F-H and Tan Z-J 2014 RNA structure prediction: progress and perspective Chin. Phys. B 23 078701
58. Reuter J S and Mathews D H 2010 RNAstructure: software for RNA secondary structure prediction and analysis BMC Bioinform. 11 129
59. Lorenz R, Bernhart S H, Höner Zu Siederdissen C, Tafer H, Flamm C, Stadler P F and Hofacker I L 2011 ViennaRNA Package 2.0 Algorithms Mol. Biol. 6 26
60. Mathews D H and Turner D H 2006 Prediction of RNA secondary structure by free energy minimization Curr. Opin. Struct. Biol. 16 270-8
61. Xu X, Zhao P and Chen S-J 2014 Vfold: a web server for RNA structure and folding thermodynamics prediction PloS One 9 e107504
62. Zuker M 2003 Mfold web server for nucleic acid folding and hybridization prediction Nucl. Acids Res. 31 3406-15
63. Xayaphoummine A, Bucher T, Thalmann F and Isambert H 2003 Prediction and statistics of pseudoknots in rna structures using exactly clustered stochastic simulations Proc. Natl Acad. Sci. USA 100 15310-5
64. Rivas E and Eddy S R 1999 A dynamic programming algorithm for RNA structure prediction including pseudoknots J. Mol. Biol. 285 2053-68
65. Theis C, Janssen S and Giegerich R 2010 Prediction of RNA secondary structure including kissing hairpin motifs Algorithms in Bioinformatics (Lecture Notes in Computer Science vol 6293) ed V Moulton and M Singh (Berlin: Springer) pp 52-64
66. Bindewald E, Kluth T and Shapiro B A 2010 Cylofold: secondary structure prediction including pseudoknots Nucl. Acids Res. 38 W368-72
67. Serra M J, Axenson T J and Turner D H 1994 A model for the stabilities of RNA hairpins based on a study of the sequence dependence of stability for hairpins of six nucleotides Biochemistry 33 14289-96
68. Liu L and Chen S-J 2010 Computing the conformational entropy for RNA folds J. Chem. Phys. 132 235104
69. Rohl C a, Strauss C E M, Misura K M S and Baker D 2004 Protein structure prediction using Rosetta Methods Enzymol. 383 66-93
70. Sripakdeevong P, Kladwang W and Das R 2011 An enumerative stepwise ansatz enables atomic-accuracy RNA loop modeling Proc. Natl Acad. Sci. USA 108 20573-8
71. Mazur A K 2003 Titration in silico of reversible B < = > A transitions in DNA J. Am. Chem. Soc. 125 7849-59
72. He Y, Maciejczyk M M, Odziej S, Scheraga H A, Liwo A, Maciejczyk M and Oldziej S 2013 Mean-field interactions between nucleic-acid-base dipoles can drive the formation of a double helix Phys. Rev. Lett. 110 098101
73. Hyeon C and Thirumalai D 2005 Mechanical unfolding of RNA hairpins Proc. Natl Acad. Sci. USA 102 6789-94
74. Cho S S, Pincus D L and Thirumalai D 2009 Assembly mechanisms of RNA pseudoknots are determined by the stabilities of constituent secondary structures Proc. Natl Acad. Sci. USA 106 17349-54
75. Morriss-Andrews A, Rottler J and Plotkin S 2010 A systematically coarse-grained model for DNA and its predictions for persistence length, stacking, twist, and chirality J. Chem. Phys. 132 35105
76. Šulc P, Romano F, Ouldridge T E, Rovigatti L, Doye J P K and Louis A A 2012 Sequence-dependent thermodynamics of a coarse-grained DNA model J. Chem. Phys. 137 135101
77. Romano F, Chakraborty D, Doye J P K, Ouldridge T E and Louis A A 2013 Coarse-grained simulations of DNA overstretching J. Chem. Phys. 138 085101
78. Xia Z, Bell D R, Shi Y and Ren P 2013 RNA 3D structure prediction by using a coarse-grained model and experimental data J. Phys. Chem. B 117 3135-44
79. Pasquali S and Derreumaux P 2010 HiRE-RNA: a high resolution coarse-grained energy model for RNA J. Phys. Chem. B 114 11957-66
80. Cragnolini T, Derreumaux P and Pasquali S 2013 Coarse-grained simulations of RNA and DNA duplexes J. Phys. Chem. B 117 8047-60
81. SantaLucia J 1998 A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics Proc. Natl Acad. Sci. USA 95 1460-5
82. Everaers R and Ejtehadi M 2003 Interaction potentials for soft and hard ellipsoids Phys. Rev. E 67 041710
83. Babadi M, Everaers R and Ejtehadi M R 2006 Coarse-grained interaction potentials for anisotropic molecules J. Chem. Phys. 124 174708
84. Lii J H and Allinger N L 1989 Molecular mechanics. The MM3 force field for hydrocarbons. 3. The van der Waals' potentials and crystal data for aliphatic and aromatic hydrocarbons J. Am. Chem. Soc. 111 8576-82
85. Zirbel C L, Sponer J E J E, Stombaugh J and Leontis N B 2009 Classification and energetics of the base-phosphate interactions in RNA Nucl. Acids Res. 37 4898-918
86. Maupetit J, Tuffery P and Derreumaux P 2007 A coarse-grained protein force field for folding and structure prediction Proteins 69 394-408
87. Pasquali S, Gan H H and Schlick T 2005 Modular RNA architecture revealed by computational analysis of existing pseudoknots and ribosomal RNAs Nucl. Acids Res. 33 1384-98
88. Izzo J, Kim N, Elmetwaly S and Schlick T 2011 RAG: an update to RNA-As-Graphs resource BMC Bioinform. 12 219
89. Sponer J, Leszczynski J and Hobza P 2002 Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases Biopolymers 61 3-31
90. Sponer J, Jurecka P and Hobza P 2004 Accurate interaction energies of hydrogen-bonded nucleic acid base pairs J. Am. Chem. Soc. 126 10142-51
91. Wang L P, Martinez T J and Pande V S 2014 Building force fields: an automatic, systematic, and reproducible approach J. Phys. Chem. Lett. 5 1885-91
92. Marrink S J and Tieleman D P 2013 Perspective on the Martini model Chem. Soc. Rev. 42 6801-22
93. Sterpone F et al 2014 The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems Chem. Soc. Rev. 43 4871-93
94. Lemieux S and Major F 2002 RNA canonical and non-canonical base pairing types: a recognition method and complete repertoire Nucl. Acids Res. 30 4250-63
95. Nguyen P H, Okamoto Y, Derreumaux P and Ngyuen P H 2013 Communication: Simulated tempering with fast on-the-fly weight determination J. Chem. Phys. 138 061102
96. Kumar S, Rosenberg J M, Bouzida D, Swendsen R H and Kollman P A 1992 THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method J. Comput. Chem. 13 1011-21
97. Chodera J D and Shirts M R 2011 Replica exchange and expanded ensemble simulations as Gibbs sampling: Simple improvements for enhanced mixing J. Chem. Phys. 135 194110
98. Earl D J and Deem M W 2005 Parallel tempering: theory, applications, and new perspectives Phys. Chem. Chem. Phys. 7 3910
99. Buchete N V and Hummer G 2008 Peptide folding kinetics from replica exchange molecular dynamics Phys. Rev. E 77 030902
100. Mitsutake A and Okamoto Y 2000 Replica-exchange simulated tempering method for simulations of frustrated systems Chem. Phys. Lett. 332 131-8
101. Park S 2008 Comparison of the serial and parallel algorithms of generalized ensemble simulations: an analytical approach Phys. Rev. E 77 016709
102. Chelli R 2010 Optimal weights in serial generalized-ensemble simulations J. Chem. Theory Comput. 6 1935-50
103. Mitsutake A and Okamoto Y 2009 From multidimensional replica-exchange method to multidimensional multicanonical algorithm and simulated tempering Phys. Rev. E 79 1-4
104. Proctor E A, Ding F and Dokholyan N V 2011 Discrete molecular dynamics Wiley Interdisciplinary Rev.: Comput. Mol. Sci. 1 80-92
105. Lv Z, Tek A, Da Silva F, Empereur-mot C, Chavent M, Baaden M and Silva F D 2013 Game on, science: How video game technology may help biologists tackle visualization challenges PloS One 8 e57990
106. Birmanns S, Rusu M and Wriggers W 2011 Using Sculptor and Situs for simultaneous assembly of atomic components into low-resolution shapes J. Struct. Biol. 173 428-35
107. Molza A-E, Férey N, Czjzek M, Le Rumeur E, Hubert J-F, Tek a, Laurent B, Baaden M and Delalande O 2014 Innovative interactive flexible docking method for multi-scale reconstruction elucidates dystrophin molecular assembly Faraday Discuss. 169 45-62
108. Surles M C, Richardson J S, Richardson D C and Brooks F P 1994 Sculpting proteins interactively: continual energy minimization embedded in a graphical modeling system Protein Sci. 3 198-210
109. Cooper S, Khatib F, Treuille A, Barbero J, Lee J, Beenen M, Leaver-Fay A, Baker D, Popović Z and Players F 2010 Predicting protein structures with a multiplayer online game Nature 466 756-60
110. Khatib F et al 2011 Crystal structure of a monomeric retroviral protease solved by protein folding game players Nat. Struct. Mol. Biol. 18 1175-7
111. Khatib F, Cooper S, Tyka M D, Xu K, Makedon I, Popovic Z, Baker D and Players F 2011 Algorithm discovery by protein folding game players Proc. Natl Acad. Sci. USA 108 18949-53
112. Lee J et al 2014 RNA design rules from a massive open laboratory Proc. Natl Acad. Sci. USA 111 2122-7
113. Delalande O, Ferey N, Grasseau G and Baaden M 2009 Complex molecular assemblies at hand via interactive simulations J. Comput. Chem. 30 2375-87
114. Humphrey W, Dalke A and Schulten K 1996 VMD: visual molecular dynamics J. Mol. Graph. 14 33-8 27-8
115. Moult J 2005 A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction Curr. Opin. Struct. Biol. 15 285-9
116. Dibrov S M, McLean J, Parsons J and Hermann T 2011 Self-assembling RNA square Proc. Natl Acad. Sci. USA 108 6405-8
117. Dibrov S, McLean J and Hermann T 2011 Structure of an RNA dimer of a regulatory element from human thymidylate synthase mRNA Acta Crystallograph. D 67 97-104
118. Huang L, Serganov A and Patel D J 2010 Structural insights into ligand recognition by a sensing domain of the cooperative glycine riboswitch Mol. Cell 40 774-86
119. Rother K, Rother M, Boniecki M, Puton T, Tomala K, Łukasz P and Bujnicki J M 2012 Template-Based, Template-Free Modeling of RNA 3D Structure: Inspirations from Protein Structure Modeling RNA 3D Structure Analysis, Prediction (Nucleic Acids, Molecular Biology vol 27) ed N Leontis and E Westhof (Berlin: Springer) chapter 5
120. Kim N K, Zhang Q, Zhou J, Theimer C A, Peterson R D and Feigon J 2008 Solution structure and dynamics of the wild-type pseudoknot of human telomerase RNA J. Mol. Biol. 384 1249-61
121. Weeks K M 2010 Advances in RNA structure analysis by chemical probing Curr. Opin. Struct. Biol. 20 295-304
122. Mathews D H, Turner D H and Zuker M 2007 RNA secondary structure prediction Current Protocols in Nucleic Acid Chemistry ed S L Beaucage et al chapter 11 unit 11.2
123. Putnam C D, Hammel M, Hura G L and Tainer J A 2007 X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution Q. Rev. Biophys. 40 191-285
124. Parisien M and Major F 2012 Determining RNA three-dimensional structures using low-resolution data J. Struct. Biol. 179 252-60
125. Mitra K and Frank J 2006 Ribosome dynamics: insights from atomic structure modeling into cryo-electron microscopy maps Ann. Rev. Biophys. Biomol. Struct. 35 299-317
126. Whitford P C, Ahmed A, Yu Y, Hennelly S P, Tama F, Spahn C M T, Onuchic J N and Sanbonmatsu K Y 2011 Excited states of ribosome translocation revealed through integrative molecular modeling Proc. Natl Acad. Sci. USA 108 18943-8
127. Lindert S, Meiler J and McCammon J A 2013 Iterative molecular dynamics-Rosetta protein structure refinement protocol to improve model quality J. Chem. Theory Comput. 9 3843-7
128. Serganov A, Yuan Y R, Pikovskaya O, Polonskaia A, Malinina L, Phan A T, Hobartner C, Micura R, Breaker R R and Patel D J 2004 Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs Chem. Biol. 11 1729-41
129. Debye P 1915 Zerstreuung von Röntgenstrahlen Ann. Phys. 351 809-23
130. Harker D 1953 The meaning of the average of |F|2 for large values of the interplanar spacing Acta Crystallograph. 6 731-6
131. Yang S, Parisien M, Major F and Roux B 2010 RNA structure determination using SAXS data J. Phys. Chem. B 114 10039-48
132. Yang S, Park S, Makowski L and Roux B 2009 A rapid coarse residue-based computational method for x-ray solution scattering characterization of protein folds and multiple conformational states of large protein complexes Biophys. J. 96 4449-63
133. Putnam D K, Lowe E W and Meiler J 2013 Reconstruction of SAXS profiles from protein structures Comput. Struct. Biotechnol. J. 8 e201308006
134. Allnér O, Nilsson L and Villa A 2012 Magnesium ion-water coordination and exchange in biomolecular simulations J. Chem. Theory Comput. 8 1493-502
135. Bowman J C, Lenz T K, Hud N V and Williams L D 2012 Cations in charge: magnesium ions in RNA folding and catalysis Curr. Opin. Struct. Biol. 22 262-72
136. Draper D E 2008 RNA folding: thermodynamic and molecular descriptions of the roles of ions Biophys. J. 95 5489-95
137. Kirmizialtin S, Silalahi A R J, Elber R and Fenley M O 2012 The ionic atmosphere around A-RNA: Poisson-Boltzmann and molecular dynamics simulations Biophys. J. 102 829-38
138. Correll C C, Wool I G and Munishkin a 1999 The two faces of the Escherichia coli 23 S rRNA sarcin/ricin domain: the structure at 1.11 A resolution J. Mol. Biol. 292 275-87
139. Reining A, Nozinovic S, Schlepckow K, Buhr F, Fürtig B and Schwalbe H 2013 Three-state mechanism couples ligand and temperature sensing in riboswitches Nature 499 355-9
140. Zhang G and Ignatova Z 2011 Folding at the birth of the nascent chain: coordinating translation with co-translational folding Curr. Opin. Struct. Biol. 21 25-31
141. Schroeder R S, Grossberger R, Picher A and Waldsich C 2002 RNA folding in vivo Curr. Opin. Struc. Biol. 12 296-300
142. Lang P T et al 2009 DOCK 6: combining techniques to model RNA-small molecule complexes RNA 15 1219-30
143. Williamson J R 2000 Induced fit in RNA-protein recognition Nat. Struct. Biol. 7 834-7
144. Schwalbe H, Buck J, Fürtig B, Noeske J and Wöhnert J 2007 Structures of RNA switches: insight into molecular recognition and tertiary structure Angew. Chem. 46 1212-9