Exploring RNA structure by integrative molecular modelling

New Biotechnology

Volumn 27, Issue 3, 2010, Pages 170-183

  Masquida, Benoît ^a   Beckert, Bertrand ^b   Jossinet, Fabrice ^a  

^a UNIVERSITÉ DE STRASBOURG   (France)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMICAL DATA; BUILDING BLOCKES; COMPARATIVE SEQUENCE ANALYSIS; INTERACTIVE PROCESS; MODELLING METHOD; MOLECULAR MODELLING; RNA MOLECULES; RNA SEQUENCES; RNA STRUCTURES; SECONDARY STRUCTURES; STRUCTURAL MOTIFS; THREE DIMENSIONS;

BIOINFORMATICS; MOLECULAR MODELING; RNA;

CRYSTAL ATOMIC STRUCTURE;

RNA;

AUTOMATION; BIOCHEMISTRY; BIOINFORMATICS; CRYSTAL STRUCTURE; MOLECULAR INTERACTION; MOLECULAR MODEL; PREDICTION; PRIORITY JOURNAL; PROTEIN MOTIF; PROTEIN SECONDARY STRUCTURE; REVIEW; RNA SEQUENCE; RNA STRUCTURE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY;

ANIMALS; BASE SEQUENCE; COMPUTATIONAL BIOLOGY; CRYSTALLOGRAPHY, X-RAY; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RNA; RNA, CATALYTIC;

EID: 77952883423     PISSN: 18716784     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.nbt.2010.02.022     Document Type: Review

References (147)

1. Kapranov P., et al. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 316 (2007) 1484-1488
2. Frith M.C., et al. The amazing complexity of the human transcriptome. Eur. J. Hum. Genet. 13 (2005) 894-897
3. Taft R.J., et al. The relationship between non-protein-coding DNA and eukaryotic complexity. Bioessays 29 (2007) 288-299
4. Tucker B.J., and Breaker R.R. Riboswitches as versatile gene control elements. Curr. Opin. Struct. Biol. 15 (2005) 342
5. Mattick J.S., and Makunin I.V. Non-coding RNA. Hum. Mol. Genet. 15 Spec No. 1 (2006) R17-R29
6. Mattick J.S. The genetic signatures of noncoding RNAs. PLoS Genet. 5 (2009) e1000459 10.1371/journal.pgen.1000459
7. Woodson S.A. Metal ions and RNA folding: a highly charged topic with a dynamic future. Curr. Opin. Chem. Biol. 9 (2005) 104-109
8. Draper D.E. RNA folding: thermodynamic and molecular descriptions of the roles of ions. Biophys. J. 95 (2008) 5489-5495
9. Sykes M.T., and Williamson J.R. A complex assembly landscape for the 30S ribosomal subunit. Annu. Rev. Biophys. 38 (2009) 197-215
10. Rajkowitsch L., et al. RNA chaperones, RNA annealers and RNA helicases. RNA Biol. 4 (2007) 118-130
11. Masquida B., and Westhof E. A modular and hierarchical approach for all-atom RNA modeling. In: Gesteland R.F., Cech T.R., and Atkins J.F. (Eds). The RNA world. third edition (2006), CSHL Press 659-681
12. Kimura M. The neutral theory of molecular evolution and the world view of the neutralists. Genome 31 (1989) 24-31
13. Cozzetto D., et al. The evaluation of protein structure prediction results. Mol. Biotechnol. 39 (2008) 1-8
14. Gutell R.R., et al. The accuracy of ribosomal RNA comparative structure models. Curr. Opin. Struct. Biol. 12 (2002) 301-310
15. Pleij C.W.A., et al. A new principle of RNA folding based on pseudoknotting. Nucl. Acids Res. 13 (1985) 1717-1731
16. Westhof E., and Jaeger L. RNA pseudoknots: Structural and functional aspects. Curr. Opin. Struct. Biol. 2 (1992) 327-333
17. Gautheret D., et al. Identification of base-triples in RNA using comparative sequence analysis. J. Mol. Biol. 248 (1995) 27-43
18. Baird N.J., et al. Structure of a folding intermediate reveals the interplay between core and peripheral elements in RNA folding. J. Mol. Biol. 352 (2005) 712-722
19. Ding F., et al. Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms. RNA 14 (2008) 1164-1173
20. Das R., and Baker D. Automated de novo prediction of native-like RNA tertiary structures. Proc. Natl. Acad. Sci. U.S.A. 104 (2007) 14664-14669
21. Parisien M., and Major F. The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data. Nature 452 (2008) 51-55
22. Jonikas M.A., et al. Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters. RNA 15 (2009) 189-199
23. Masquida B., and Westhof E. Modeling the architecture of structured RNAs within a modular and hierarchical framework. In: Hartmann R.K., Bindereif A., Schön A., and Westhof E. (Eds). Handbook of RNA biochemistry (2005), Wiley VCH Verlag Gmbh & Co. 536-545
24. Michel F., and Westhof E. Modelling of the three-dimensional architecture of group-I catalytic introns based on comparative sequence analysis. J. Mol. Biol. 216 (1990) 585-610
25. Massire C., and Westhof E. MANIP: an interactive tool for modelling RNA. J. Mol. Graph. Model. 16 (1998) 197-205, 255-257
26. Westhof E., et al. RNA tectonics: towards RNA design. Fold. Des. 1 (1996) R78-R88
27. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31 (2003) 3406-3415
28. Hofacker I.L., et al. Fast folding and comparison of RNA secondary structures. Monatshefte für Chemie/Chem. Monthly 125 (1994) 167-188
29. Xayaphoummine A., et al. Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations. Proc. Natl. Acad. Sci. U.S.A. 100 (2003) 15310-15315
30. Rivas E., and Eddy S.R. The language of RNA: a formal grammar that includes pseudoknots. Bioinformatics 16 (2000) 334-340
31. Reeder J., and Giegerich R. Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics. BMC Bioinformatics 5 (2004) 104
32. Jossinet F., et al. RNA structure: bioinformatic analysis. Curr. Opin. Microbiol. 10 (2007) 279-285
33. Tabei Y., et al. SCARNA: fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments. Bioinformatics 22 (2006) 1723-1729
34. Dalli D., et al. STRAL: progressive alignment of non-coding RNA using base pairing probability vectors in quadratic time. Bioinformatics 22 (2006) 1593-1599
35. Siebert S., and Backofen R. MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons. Bioinformatics 21 (2005) 3352-3359
36. Sankoff D. Simultaneous solution of the RNA folding. Alignment and protosequence problems. SIAM J. Appl. Math. 45 (1985) 810-825
37. Gorodkin J., et al. Finding the most significant common sequence and structure motifs in a set of RNA sequences. Nucleic Acids Res. 25 (1997) 3724-3732
38. Havgaard J.H., et al. The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search. Nucleic Acids Res. 33 Web Server issue (2005) W650-W653
39. Mathews D.H. Predicting a set of minimal free energy RNA secondary structures common to two sequences. Bioinformatics 21 (2005) 2246-2253
40. Gardner P.P., et al. Rfam: updates to the RNA families database. Nucleic Acids Res. 37 Suppl. 1 (2009) D136-140
41. Seibel P.N., et al. 4SALE-a tool for synchronous RNA sequence and secondary structure alignment and editing. BMC Bioinformatics 7 (2006) 498
42. Wilm A., et al. ConStruct: improved construction of RNA consensus structures. BMC Bioinformatics 9 (2008) 219
43. Jossinet F., and Westhof E. Sequence to structure (S2S): display, manipulate and interconnect RNA data from sequence to structure. Bioinformatics 21 (2005) 3320-3321
44. Andersen E.S., et al. Semiautomated improvement of RNA alignments. RNA 13 (2007) 1850-1859
45. Cannone J.J., et al. The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics 3 (2002) 2
46. Andronescu M., et al. RNA STRAND: the RNA secondary structure and statistical analysis database. BMC Bioinformatics 9 (2008) 340
47. Berman H.M., et al. The nucleic acid database. Methods Biochem. Anal. 44 (2003) 199-216
48. Yang H., et al. Tools for the automatic identification and classification of RNA base pairs. Nucleic Acids Res. 31 (2003) 3450-3460
49. Lemieux S., and Major F. RNA canonical and non-canonical base pairing types: a recognition method and complete repertoire. Nucleic Acids Res. 30 (2002) 4250-4263
50. Soukup G.A., and Breaker R.R. Relationship between internucleotide linkage geometry and the stability of RNA. RNA 5 (1999) 1308-1325
51. Watts J.M., et al. Architecture and secondary structure of an entire HIV-1 RNA genome. Nature 460 (2009) 711-716
52. Brunel C., and Romby P. Probing RNA structure and RNA-ligand complexes with chemical probes. Methods Enzymol. 318 (2000) 3-21
53. Leontis N.B., and Westhof E. Geometric nomenclature and classification of RNA base pairs. RNA 7 (2001) 499-512
54. Leontis N.B., et al. The non-Watson-Crick base pairs and their associated isostericity matrices. Nucleic Acids Res. 30 (2002) 3497-3531
55. Stombaugh J., et al. Frequency and isostericity of RNA base pairs. Nucleic Acids Res. 37 (2009) 2294-2312
56. Leontis N.B., et al. Motif prediction in ribosomal RNAs Lessons and prospects for automated motif prediction in homologous RNA molecules. Biochimie 84 (2002) 961-973
57. Branch A.D., et al. Ultraviolet light-induced crosslinking reveals a unique region of local tertiary structure in potato spindle tuber viroid and HeLa 5S RNA. Proc. Natl. Acad. Sci. U.S.A. 82 (1985) 6590-6594
58. Leontis N.B., and Westhof E. A common motif organizes the structure of multi-helix loops in 16S and 23S ribosomal RNAs. J. Mol. Biol. 283 (1998) 571-583
59. Ban N., et al. The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution. Science 289 (2000) 905-920
60. Wimberly B.T., et al. Structure of the 30S ribosomal subunit. Nature 407 (2000) 327-339
61. Earnshaw D.J., et al. Inter-domain cross-linking and molecular modelling of the hairpin ribozyme. J. Mol. Biol. 274 (1997) 197-212
62. Collier A.J., et al. A conserved RNA structure within the HCV IRES eIF3-binding site. Nat. Struct. Biol. 9 (2002) 375-380
63. Waldsich C., et al. Monitoring intermediate folding states of the td group I intron in vivo. EMBO J. 21 (2002) 5281-5291
64. Klein D.J., et al. The kink-turn: a new RNA secondary structure motif. EMBO J. 20 (2001) 4214-4221
65. Lescoute A., et al. Recurrent structural RNA motifs, Isostericity matrices and sequence alignments. Nucleic Acids Res. 33 (2005) 2395-2409
66. Cate J.H., et al. Crystal structure of a group I ribozyme domain: principles of RNA packing. Science 273 (1996) 1678-1684
67. Lescoute A., and Westhof E. Topology of three-way junctions in folded RNAs. RNA 12 (2006) 83-93
68. Steinberg S.V., and Boutorine Y.I. G-ribo motif favors the formation of pseudoknots in ribosomal RNA. RNA 13 (2007) 1036-1042
69. Steinberg S.V., and Boutorine Y.I. G-ribo: a new structural motif in ribosomal RNA. RNA 13 (2007) 549-554
70. Laing C., et al. Tertiary motifs revealed in analyses of higher-order RNA junctions. J. Mol. Biol. 393 (2009) 67-82
71. Jaeger L., et al. The UA_handle: a versatile submotif in stable RNA architectures. Nucleic Acids Res. 37 (2009) 215-230
72. Wimberly B.T., et al. A detailed view of a ribosomal active site: the structure of the L11-RNA complex [see comments]. Cell 97 (1999) 491-502
73. Conn G.L., et al. The crystal structure of the RNA/DNA hybrid r(GAAGAGAAGC)center dot d(GCTTCTCTTC) shows significant differences to that found in solution. Nucleic Acid Res. 27 (1999) 555-561
74. Suddath F.L., et al. Three-dimensional structure of yeast phenylalanine transfer RNA at 3.0angstroms resolution. Nature 248 (1974) 20-24
75. Robertus J.D., et al. Structure of yeast phenylalanine tRNA at 3 Å resolution. Nature 250 (1974) 546-551
76. Asp. Nature 288 (1980) 669-674
77. Krasilnikov A.S., and Mondragon A. On the occurrence of the T-loop RNA folding motif in large RNA molecules. RNA 9 (2003) 640-643
78. Krasilnikov A.S., et al. Basis for structural diversity in homologous RNAs. Science 306 (2004) 104-107
79. Lu M., and Steitz T.A. Structure of Escherichia coli ribosomal protein L25 complexed with a 5S rRNA fragment at 1.8-Å resolution. Proc. Natl. Acad. Sci. U.S.A. 97 (2000) 2023-2028
80. Torres-Larios A., et al. Structural basis of translational control by Escherichia coli threonyl tRNA synthetase. Nat. Struct. Biol. 9 (2002) 343-347
81. Woese C.R., et al. Architecture of ribosomal RNA: constraints on the sequence of "tetra-loops". Proc. Natl. Acad. Sci. U.S.A. 87 (1990) 8467-8471
82. Toor N., et al. Crystal structure of a self-spliced group II intron. Science 320 (2008) 77-82
83. Keating K.S., et al. The GANC tetraloop: a novel motif in the group IIC intron structure. J. Mol. Biol. 383 (2008) 475-481
84. Pley H.W., et al. Model for an RNA tertiary interaction from the structure of an intermolecular complex between a GAAA tetraloop and an RNA helix. Nature 372 (1994) 111-113
85. Nissen P., et al. RNA tertiary interactions in the large ribosomal subunit: the A-minor motif. Proc. Natl. Acad. Sci. U.S.A. 98 (2001) 4899-4903
86. Lee J.C., et al. The UAA/GAN internal loop motif: a new RNA structural element that forms a cross-strand AAA stack and long-range tertiary interactions. J. Mol. Biol. 360 (2006) 978-988
87. Doherty E.A., et al. A universal mode of helix packing in RNA. Nat. Struct. Biol. 8 (2001) 339-343
88. Kondo J., et al. Two conformational states in the crystal structure of the Homo sapiens cytoplasmic ribosomal decoding A site. Nucleic Acids Res. 34 (2006) 676-685
89. Djelloul M., and Denise A. Automated motif extraction and classification in RNA tertiary structures. RNA 14 (2008) 2489-2497
90. Sarver M., et al. FR3D: finding local and composite recurrent structural motifs in RNA 3D structures. J. Math. Biol. 56 (2008) 215-252
91. Tamura M., et al. SCOR: structural Classification of RNA, version 2.0. Nucleic Acids Res. 32 Database issue (2004) D182-D184
92. Fera D., et al. RAG: RNA-As-Graphs web resource. BMC Bioinformatics 5 (2004) 88
93. Gan H.H., et al. RAG: RNA-As-Graphs database-concepts, analysis, and features. Bioinformatics 20 (2004) 1285-1291
94. Abraham M., et al. Analysis and classification of RNA tertiary structures. RNA 14 (2008) 2274-2289
95. Nagaswamy U., et al. NCIR: a database of non-canonical interactions in known RNA structures. Nucleic Acids Res. 30 (2002) 395-397
96. Chworos A., et al. Building programmable jigsaw puzzles with RNA. Science 306 (2004) 2068-2072
97. Gautheret D., et al. A major family of motifs involving G.A mismatches in ribosomal RNA. J. Mol. Biol. 242 (1994) 1-8
98. Elgavish T., et al. AA.AG@helix.ends: A:A and A:G base-pairs at the ends of 16 S and 23 S rRNA helices. J. Mol. Biol. 310 (2001) 735-753
99. Cate J.H., et al. RNA tertiary structure mediation by adenosine platforms. Science 273 (1996) 1696-1699
100. Westhof E., et al. Crystallographic refinement of yeast aspartic acid transfer RNA. J. Mol. Biol. 184 (1985) 119-145
101. Mangalam H. The Bio* toolkits-a brief overview. Brief Bioinform. 3 (2002) 296-302
102. Curcin V., et al. Web services in the life sciences. Drug Discov. Today 10 (2005) 865-871
103. Stein L. Creating a bioinformatics nation. Nature 417 (2002) 119-120
104. Carugo O., and Pongor S. A normalized root-mean-square distance for comparing protein three-dimensional structures. Protein Sci. 10 (2001) 1470-1473
105. Kleywegt G.J. Use of non-crystallographic symmetry in protein structure refinement. Acta Cryst. D52 (1996) 842-857
106. Parisien M., et al. New metrics for comparing and assessing discrepancies between RNA 3D structures and models. RNA 15 (2009) 1875-1885
107. Rangan P., et al. Architecture and folding mechanism of the Azoarcus Group I Pre-tRNA. J. Mol. Biol. 339 (2004) 41-51
108. Michel F., et al. The guanosine binding site of the tetrahymena ribozyme. Nature 342 (1989) 391-395
109. Adams P.L., et al. Crystal structure of a self-splicing group I intron with both exons. Nature 430 (2004) 45-50
110. Strobel S.A., et al. RNA kink turns to the left and to the right. RNA 10 (2004) 1852-1854
111. Beckert B., et al. Molecular modelling of the GIR1 branching ribozyme gives new insight into evolution of structurally related ribozymes. EMBO J. 27 (2008) 667-678
112. Nielsen H., et al. An mRNA is capped by a 2′, 5′ lariat catalyzed by a group I-like ribozyme. Science 309 (2005) 1584-1587
113. Guo F., et al. Structure of the tetrahymena ribozyme; base triple sandwich and metal ion at the active site. Mol. Cell 16 (2004) 351-362
114. Golden B.L., et al. Crystal structure of a phage Twort group I ribozyme-product complex. Nat. Struct. Mol. Biol. 12 (2005) 82-89
115. Lehnert V., et al. New loop-loop tertiary interactions in self-splicing introns of subgroup IC and ID: a complete 3D model of the Tetrahymena thermophila ribozyme. Chem. Biol. 3 (1996) 993-1009
116. Caprara M.G., et al. A Tyrosyl-tRNA synthetase protein induces tertiary folding of the group I intron catalytic core. J. Mol. Biol. 257 (1996) 512-531
117. Rangan P., et al. Assembly of core helices and rapid tertiary folding of a small bacterial group I ribozyme. Proc. Natl. Acad. Sci. U.S.A. 100 (2003) 1574-1579
118. Paukstelis P.J., et al. Structure of a tyrosyl-tRNA synthetase splicing factor bound to a group I intron RNA. Nature 451 (2008) 94-97
119. Krol A., et al. Solution structure of human U1 snRNA. Derivation of a possible three-dimensional model. Nucleic Acids Res. 18 (1990) 3803-3811
120. Pomeranz Krummel D.A., et al. Crystal structure of human spliceosomal U1 snRNP at 5.5 Å resolution. Nature 458 (2009) 475-480
121. Brunel C., et al. Three-dimensional model of E. coli ribosomal 5S RNA as deduced from structure probing in solution and computer modeling. J. Mol. Biol. 221 (1991) 293-308
122. Tuschl T., et al. A three-dimensional model for the hammerhead ribozyme based on fluorescence measurements. Science 266 (1994) 785-789
123. Pley H.W., et al. Three-dimensional structure of a hammerhead ribozyme. Nature 372 November (1994) 68-74
124. Scott W.G., et al. The crystal structure of an all-RNA hammerhead ribozyme: a proposed mechanism for RNA catalytic cleavage. Cell 81 (1995) 991-1002
125. Tanner N.K., et al. A three-dimensional model of hepatitis delta virus ribozyme based on biochemical and mutational analysis. Curr. Biol. 4 (1994) 488-498
126. Ferré-D'Amaré A.R., et al. Crystal structure of a hepatitis delta virus ribozyme. Nature 395 (1998) 567-574
127. Rupert P.B., and Ferre-D'Amare A.R. Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis. Nature 410 (2001) 780-786
128. Keiper S., et al. Architecture of a Diels-Alderase ribozyme with a preformed catalytic pocket. Chem. Biol. 11 (2004) 1217-1227
129. Serganov A., et al. Structural basis for Diels-Alder ribozyme-catalyzed carbon-carbon bond formation. Nat. Struct. Mol. Biol. 12 (2005) 218-224
130. Bergman N.H., et al. The three-dimensional architecture of the class I ligase ribozyme. RNA 10 (2004) 176-184
131. 2+ dependence: Selection, sequence analysis, and identification of functional tertiary interactions. RNA 15 (2009) 2129-2146
132. Masquida B., et al. Context dependent RNA-RNA recognition in a three-dimensional model of the 16S rRNA core. Bioorgan. Med. Chem. 5 (1997) 1021-1035
133. Serganov A.A., et al. The 16S rRNA binding site of Thermus thermophilus ribosomal protein S15: comparison with Escherichia coli S15, minimum site and structure. RNA 2 (1996) 1124-1138
134. Nikulin A., et al. Crystal structure of the S15-rRNA complex. Nat. Struct. Biol. 7 (2000) 273-277
135. Schuwirth B.S., et al. Structures of the bacterial ribosome at 3.5 Å resolution. Science 310 (2005) 827-834
136. Caillet J., et al. The modular structure of Escherichia coli threonyl-tRNA synthetase as both an enzyme and a regulator of gene expression. Mol. Microbiol. 47 (2003) 961-974
137. Massire C., et al. Derivation of the three-dimensional architecture of bacterial ribonuclease P RNAs from comparative sequence analysis. J. Mol. Biol. 279 (1998) 773-793
138. Tsai H.Y., et al. Molecular modeling of the three-dimensional structure of the bacterial RNase P holoenzyme. J. Mol. Biol. 325 (2003) 661-675
139. Krasilnikov A.S., et al. Crystal structure of the specificity domain of ribonuclease P. Nature 421 (2003) 760-764
140. Torres-Larios A., et al. Crystal structure of the RNA component of bacterial ribonuclease P. Nature 437 (2005) 584-587
141. Kazantsev A.V., et al. Crystal structure of a bacterial ribonuclease P RNA. Proc. Natl. Acad. Sci. U.S.A. 102 (2005) 13392-13397
142. Costa M., et al. A three-dimensional perspective on exon binding by a group II self-splicing intron. EMBO J. 19 (2000) 5007-5018
143. Shi H., and Moore P.B. The crystal structure of yeast phenylalanine tRNA at 1.93 Å resolution: a classic structure revisited. RNA 6 (2000) 1091-1105
144. Klein D.J., et al. The roles of ribosomal proteins in the structure assembly, and evolution of the large ribosomal subunit. J. Mol. Biol. 340 (2004) 141-177
145. Szep S., et al. The crystal structure of a 26-nucleotide RNA containing a hook-turn. RNA 9 (2003) 44-51
146. Correll C.C., et al. The two faces of the Escherichia coli 23 S rRNA sarcin/ricin domain: the structure at 1.11 A resolution. J. Mol. Biol. 292 (1999) 275-287
147. Correll C.C., et al. Metals, motifs, and recognition in the crystal structure of a 5S rRNA domain. Cell 28 (1997) 705-712