Determining RNA three-dimensional structures using low-resolution data

Journal of Structural Biology

Volumn 179, Issue 3, 2012, Pages 252-260

  Parisien, Marc ^a   Major, François ^b  

^a UNIVERSITY OF CHICAGO   (United States)

^b INSTITUTE FOR RESEARCH IN IMMUNOLOGY AND CANCER   (Canada)

Author keywords

3 D; Footprinting; Low resolution; MC Fold; MC Sym; MOHCA; MPE; RNA; SAXS; Structure

Indexed keywords

AC; BACTERIAL RNA; EDETIC ACID; HYDROXYL RADICAL; TRANSFER RNA; UNCLASSIFIED DRUG;

ACCURACY; ARTICLE; ATOM; CONTROLLED STUDY; ESCHERICHIA COLI; INTRON; NONHUMAN; PRIORITY JOURNAL; PROTEIN FOOTPRINTING; RNA ANALYSIS; RNA STRUCTURE; STRUCTURE ANALYSIS; TETRAHYMENA THERMOPHILA; X RAY CRYSTALLOGRAPHY;

BASE SEQUENCE; COMPUTER SIMULATION; DATA INTERPRETATION, STATISTICAL; ESCHERICHIA COLI; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RNA, BACTERIAL; RNA, TRANSFER, VAL;

ESCHERICHIA COLI; TETRAHYMENA THERMOPHILA;

EID: 84865187135     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2011.12.024     Document Type: Article

References (68)

1. Ali M., Lipfert J., Seifert S., Herschlag D., Doniach S. The ligand-free state of the TPP riboswitch: a partially folded RNA structure. J. Mol. Biol. 2010, 396:153-165.
2. Auffinger P., Hashem Y. Nucleic acid solvation: from outside to insight. Curr. Opin. Struct. Biol. 2007, 17:325-333.
3. Bailor M.H., Sun X., Al-Hashimi H.M. Topology links RNA secondary structure with global conformation, dynamics, and adaptation. Science 2010, 327:202-206.
4. Bailor M.H., Mustoe A.M., Brooks C.L., Al-Hashimi H.M. Topological constraints: using RNA secondary structure to model 3D conformation, folding pathways, and dynamic adaptation. Curr. Opin. Struct. Biol. 2011, 21:296-305.
5. Bouchard P., Lacroix-Labonte J., Desjardins G., Lampron P., Lisi V., et al. Role of SLV in SLI substrate recognition by the Neurospora VS ribozyme. Rna-a Publication of the Rna Society 2008, 14:736-748.
6. Cao S., Chen S.J. Physics-based de novo prediction of RNA 3D structures. J. Phys. Chem. 2011, 115:4216-4226.
7. Cate J.H., Gooding A.R., Podell E., Zhou K.H., Golden B.L., et al. Crystal structure of a group I ribozyme domain: principles of RNA packing. Science 1996, 273:1678-1685.
8. Cate J.H., Gooding A.R., Podell E., Zhou K., Golden B.L., et al. RNA tertiary structure mediation by adenosine platforms. Science 1996, 273:1696-1699.
9. Chu V.B., Lipfert J., Bai Y., Pande V.S., Doniach S., et al. Do conformational biases of simple helical junctions influence RNA folding stability and specificity?. RNA 2009, 15:2195-2205.
10. Costa M., Michel F. Frequent use of the same tertiary motif by self-folding Rnas. EMBO J. 1995, 14:1276-1285.
11. Crick F. Central dogma of molecular biology. Nature 1970, 227:561-563.
12. Das R., Baker D. Automated de novo prediction of native-like RNA tertiary structures. Proc. Natl. Acad. Sci. USA 2007, 104:14664-14669.
13. Das R., Kudaravalli M., Jonikas M., Laederach A., Fong R., et al. Structural inference of native and partially folded RNA by high-throughput contact mapping. Proc. Natl. Acad. Sci. USA 2008, 105:4144-4149.
14. Debye P. Dispersion of rontgen rays. Ann. Phys. 1915, 46:809-823.
15. Deigan K.E., Li T.W., Mathews D.H., Weeks K.M. Accurate SHAPE-directed RNA structure determination. Proc. Natl. Acad. Sci. USA 2009, 106:97-102.
16. Ding F., Sharma S., Chalasani P., Demidov V.V., Broude N.E., et al. Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms. RNA 2008, 14:1164-1173.
17. Draper D.E., Grilley D., Soto A.M. Ions and RNA folding. Annu. Rev. Biophys. Biomol. Struct. 2005, 34:221-243.
18. Fang X., Littrell K., Yang X.J., Henderson S.J., Siefert S., et al. Mg2+-dependent compaction and folding of yeast tRNAPhe and the catalytic domain of the B. subtilis RNase P RNA determined by small-angle X-ray scattering. Biochemistry 2000, 39:11107-11113.
19. Fuller W., Hodgson A. Conformation of the anticodon loop in tRNA. Nature 1967, 215:817-821.
20. Gherghe C.M., Leonard C.W., Ding F., Dokholyan N.V., Weeks K.M. Native-like RNA tertiary structures using a sequence-encoded cleavage agent and refinement by discrete molecular dynamics. J. Am. Chem. Soc. 2009, 131:2541-2546.
21. Ginalski K., Grishin N.V., Godzik A., Rychlewski L. Practical lessons from protein structure prediction. Nucleic Acids Res. 2005, 33:1874-1891.
22. Grishaev A., Ying J., Canny M.D., Pardi A., Bax A. Solution structure of tRNAVal from refinement of homology model against residual dipolar coupling and SAXS data. J. Biomol. NMR 2008, 42:99-109.
23. Han H., Dervan P.B. Visualization of RNA tertiary structure by RNA-EDTA.Fe(II) autocleavage: analysis of tRNA(Phe) with uridine-EDTA. Fe(II) at position 47. Proc. Natl. Acad. Sci. USA 1994, 91:4955-4959.
24. Jaeger L., Michel F., Westhof E. Involvement of a Gnra tetraloop in long-range tertiary interactions. J. Mol. Biol. 1994, 236:1271-1276.
25. Jaeger L., Verzemnieks E.J., Geary C. The UA_handle: a versatile submotif in stable RNA architectures. Nucleic Acids Res. 2009, 37:215-230.
26. Jonikas M.A., Radmer R.J., Altman R.B. Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural models. Bioinformatics 2009, 25:3259-3266.
27. Jonikas M.A., Radmer R.J., Laederach A., Das R., Pearlman S., et al. Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters. RNA 2009, 15:189-199.
28. Kim J., Yu S., Shim B., Kim H., Min H., et al. A robust peak detection method for RNA structure inference by high-throughput contact mapping. Bioinformatics 2009, 25:1137-1144.
29. Klingler T.M., Brutlag D.L. Detection of correlations in tRNA sequences with structural implications. Proc. Int. Conf. Intell. Syst. Mol. Biol. 1993, 1:225-233.
30. Koch M.H., Vachette P., Svergun D.I. Small-angle scattering: a view on the properties, structures and structural changes of biological macromolecules in solution. Q Rev. Biophys. 2003, 36:147-227.
31. Krasilnikov A.S., Mondragon A. On the occurrence of the T-loop RNA folding motif in large RNA molecules. RNA 2003, 9:640-643.
32. Laing C, Schlick T (2010) Computational approaches to 3D modeling of RNA. Journal of Physics-Condensed Matter 22.
33. Latham J.A., Cech T.R. Defining the inside and outside of a catalytic RNA molecule. Science 1989, 245:276-282.
34. Lee J.C., Cannone J.J., Gutell R.R. The lonepair triloop: a new motif in RNA structure. J. Mol. Biol. 2003, 325:65-83.
35. Lemieux S., Major F. Automated extraction and classification of RNA tertiary structure cyclic motifs. Nucleic Acids Res. 2006, 34:2340-2346.
36. Lemieux S., Chartrand P., Cedergren R., Major F. Modeling active RNA structures using the intersection of conformational space: application to the lead-activated ribozyme. RNA 1998, 4:739-749.
37. Levitt M. Detailed molecular model for transfer ribonucleic acid. Nature 1969, 224:759-763.
38. Lipfert J., Doniach S. Small-angle X-ray scattering from RNA, proteins, and protein complexes. Annu. Rev. Biophys. Biomol. Struct. 2007, 36:307-327.
39. Lipfert J., Chu V.B., Bai Y., Herschlag D., Doniach S. Low-Resolution Models for Nucleic Acids from Small-Angle X-ray Scattering with Applications to Electrostatic Modeling. J. Appl. Crystallogr. 2007, 40:s229-s234.
40. Major F. Building three-dimensional ribonucleic acid structures. Comput. Sci. Eng. 2003, 5:44-53.
41. Major F., Turcotte M., Gautheret D., Lapalme G., Fillion E., et al. The combination of symbolic and numerical computation for three-dimensional modeling of RNA. Science 1991, 253:1255-1260.
42. Major F., Gautheret D., Cedergren R. Reproducing the three-dimensional structure of a tRNA molecule from structural constraints. Proc. Natl. Acad. Sci. USA 1993, 90:9408-9412.
43. Martinez H.M., Maizel J.V., Shapiro B.A. RNA2D3D: a program for generating, viewing, and comparing 3-dimensional models of RNA. J. Biomol. Struct. Dyn. 2008, 25:669-683.
44. Merino E.J., Wilkinson K.A., Coughlan J.L., Weeks K.M. RNA structure analysis at single nucleotide resolution by selective 2'-hydroxyl acylation and primer extension (SHAPE). J. Am. Chem. Soc. 2005, 127:4223-4231.
45. Michel F., Westhof E. Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J. Mol. Biol. 1990, 216:585-610.
46. Mitra S., Shcherbakova I.V., Altman R.B., Brenowitz M., Laederach A. High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis. Nucleic Acids Res. 2008, 36:e63.
47. Mortimer S.A., Weeks K.M. A fast-acting reagent for accurate analysis of RNA secondary and tertiary structure by SHAPE chemistry. J. Am. Chem. Soc. 2007, 129:4144-4145.
48. Murphy F.L., Cech T.R. Gaaa tetraloop and conserved bulge stabilize tertiary structure of a group-I intron domain. J. Mol. Biol. 1994, 236:49-63.
49. Nilsson L., Rigler R., Laggner P. Structural variability of tRNA: small-angle x-ray scattering of the yeast tRNAphe-Escherichia coli tRNAGlu2 complex. Proc. Natl. Acad. Sci. USA 1982, 79:5891-5895.
50. Parisien M., Major F. The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data. Nature 2008, 452:51-55.
51. Reymond C., Levesque D., Bisaillon M., Perreault J.P. Developing three-dimensional models of putative-folding intermediates of the HDV ribozyme. Structure 2010, 18:1608-1616.
52. Sanner M.F., Olson A.J., Spehner J.C. Reduced surface: an efficient way to compute molecular surfaces. Biopolymers 1996, 38:305-320.
53. Sharma S., Ding F., Dokholyan N.V. IFoldRNA: three-dimensional RNA structure prediction and folding. Bioinformatics 2008, 24:1951-1952.
54. Sharp P.A. The centrality of RNA. Cell 2009, 136:577-580.
55. Sim A.Y., Levitt M. Clustering to identify RNA conformations constrained by secondary structure. Proc. Natl. Acad. Sci. USA 2011, 108:3590-3595.
56. Svergun D.I. Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing (vol 76, pg 2879, 1999). Biophys. J. 1999, 77:2896.
57. Svergun D.I., Semenyuk A.V., Feigin L.A. Small-angle-scattering-data treatment by the regularization method. Acta Crystallographica Section A 1988, 44:244-250.
58. Svergun D., Barberato C., Koch M.H.J. CRYSOL - A program to evaluate x-ray solution scattering of biological macromolecules from atomic coordinates. J. Appl. Crystallogr. 1995, 28:768-773.
59. Takamoto K., Das R., He Q., Doniach S., Brenowitz M., et al. Principles of RNA compaction: insights from the equilibrium folding pathway of the P4-P6 RNA domain in monovalent cations. J. Mol. Biol. 2004, 343:1195-1206.
60. Tullius T.D., Greenbaum J.A. Mapping nucleic acid structure by hydroxyl radical cleavage. Curr. Opin. Chem. Biol. 2005, 9:127-134.
61. Tyagi R., Mathews D.H. Predicting helical coaxial stacking in RNA multibranch loops. RNA 2007, 13:939-951.
62. Wang Z., Parisien M., Scheets K., Miller W.A. The cap-binding translation initiation factor, eIF4E, binds a pseudoknot in a viral cap-independent translation element. Structure 2011, 19:868-880.
63. Wilkinson K.A., Gorelick R.J., Vasa S.M., Guex N., Rein A., et al. High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states. PLoS Biol. 2008, 6:e96.
64. Williamson J.R. Induced fit in RNA-protein recognition. Nat. Struct. Biol. 2000, 7:834-837.
65. Yang S.C., Park S., Makowski L., Roux B. 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. 2009, 96:4449-4463.
66. Yang S., Parisien M., Major F., Roux B. RNA structure determination using SAXS data. J. Phys. Chem. B 2010, 114:10039-10048.
67. Zemla A, Venclovas C, Moult J, Fidelis K (1999) Processing and analysis of CASP3 protein structure predictions. Proteins-Structure Function and Genetics: 22-29.
68. Zhuang Z., Jaeger L., Shea J.E. Probing the structural hierarchy and energy landscape of an RNA T-loop hairpin. Nucleic Acids Res. 2007, 35:6995-7002.