An enumerative stepwise ansatz enables atomic-accuracy RNA loop modeling

Proceedings of the National Academy of Sciences of the United States of America

Volumn 108, Issue 51, 2011, Pages 20573-20578

  Sripakdeevong, Parin ^a   Kladwang, Wipapat ^a   Das, Rhiju ^a  

^a STANFORD UNIVERSITY   (United States)

Author keywords

De novo modeling; Dynamic programming; Nucleic acid; Structure mapping; Tertiary structure

Indexed keywords

MONOMER; RIBOZYME; RNA;

ACCURACY; ARTICLE; ATOM; CONCEPTUAL FRAMEWORK; ENERGY RECOVERY; HYPOTHESIS; MONTE CARLO METHOD; PRIORITY JOURNAL; PROTEIN MOTIF; PROTEIN TERTIARY STRUCTURE; RIBOSOME; RIBOSWITCH; RNA CONFORMATION; RNA LOOP; ROSETTA FRAMEWORK; STEPWISE ANSATZ;

AMINO ACID MOTIFS; COMPUTER SIMULATION; COMPUTERS; CRYSTALLOGRAPHY, X-RAY; MODELS, MOLECULAR; MONTE CARLO METHOD; NUCLEIC ACID CONFORMATION; NUCLEOTIDE MOTIFS; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; REPRODUCIBILITY OF RESULTS; RIBOSOMES; RNA; RNA, CATALYTIC; SOFTWARE;

EID: 84855480988     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1106516108     Document Type: Article

References (46)

1. Bradley P, Misura KM, Baker D (2005) Toward high-resolution de novo structure prediction for small proteins. Science 309:1868-1871. (Pubitemid 41325099)
2. Jones DT, et al. (2005) Prediction of novel and analogous folds using fragment assembly and fold recognition. Proteins 61(Suppl 7):143-151. (Pubitemid 43069968)
3. Qian B, et al. (2007) High-resolution structure prediction and the crystallographic phase problem. Nature 450:259-264. (Pubitemid 350100534)
4. Fleishman SJ, et al. (2010) Rosetta in CAPRI rounds 13-19. Proteins 78:3212-3218.
5. Ashworth J, et al. (2006) Computational redesign of endonuclease DNA binding and cleavage specificity. Nature 441:656-659. (Pubitemid 43927299)
6. Levinthal C (1968) Are there pathways for protein folding? J Chim Phys 65:44-45.
7. Kim DE, Blum B, Bradley P, Baker D (2009) Sampling bottlenecks in de novo protein structure prediction. J Mol Biol 393:249-260.
8. Jucker FM, Heus HA, Yip PF, Moors EH, Pardi A (1996) A network of heterogeneous hydrogen bonds in GNRA tetraloops. J Mol Biol 264:968-980. (Pubitemid 27019486)
9. Das R (2011) Four small puzzles that Rosetta doesn't solve. PLoS One 6:e20044.
10. Das R, Karanicolas J, Baker D (2010) Atomic accuracy in predicting and designing noncanonical RNA structure. Nat Methods 7:291-294.
11. Schudoma C, May P, Nikiforova V, Walther D (2010) Sequence-structure relationships in RNA loops: Establishing the basis for loop homology modeling. Nucleic Acids Res 38:970-980.
12. Rother M, Rother K, Puton T, Bujnicki JM (2011) ModeRNA: a tool for comparative modeling of RNA 3D structure. Nucleic Acids Res 39:4007-4022.
13. Das R, Baker D (2007) Automated de novo prediction of native-like RNA tertiary structures. Proc Natl Acad Sci USA 104:14664-14669. (Pubitemid 350003200)
14. Parisien M, Major F (2008) The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data. Nature 452:51-55. (Pubitemid 351355097)
15. Flores SC, Altman RB (2010) Turning limited experimental information into 3D models of RNA. RNA 16:1769-1778.
16. Cao S, Chen SJ (2011) Physics-based de novo prediction of RNA 3D structures. J Phys Chem B 115:4216-4226.
17. Gibson KD, Scheraga HA (1987) Revised algorithms for the build-up procedure for predicting protein conformations by energy minimization. J Comput Chem 8:826-834.
18. Hockenmaier J, Joshi AK, Dill KA (2007) Routes are trees: The parsing perspective on protein folding. Proteins 66(1):1-15. (Pubitemid 44955974)
19. Shell MS, Ozkan SB, Voelz V, Wu GA, Dill KA (2009) Blind test of physics-based prediction of protein structures. Biophys J 96:917-924.
20. Moult J, Fidelis K, Kryshtafovych A, Rost B, Tramontano A (2009) Critical assessment of methods of protein structure prediction - round VIII. Proteins 77(Suppl 9):1-4.
21. Costa M, Michel F (1997) Rules for RNA recognition of GNRA tetraloops deduced by in vitro selection: Comparison with in vivo evolution. EMBO J 16:3289-3302. (Pubitemid 27234966)
22. Geary C, Baudrey S, Jaeger L (2008) Comprehensive features of natural and in vitro selected GNRA tetraloop-binding receptors. Nucleic Acids Res 36:1138-1152. (Pubitemid 351330932)
23. Leontis NB, Westhof E (2001) Geometric nomenclature and classification of RNA base pairs. RNA 7:499-512. (Pubitemid 32416808)
24. Richardson JS, et al. (2008) RNA backbone: Consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution). RNA 14:465-481. (Pubitemid 351397812)
25. Kortemme T, Kim DE, Baker D (2004) Computational alanine scanning of protein-protein interfaces. Sci STKE 2004:pl2.
26. Smith TF, Waterman MS, Fitch WM (1981) Comparative biosequence metrics. J Mol Evol 18:38-46.
27. Zuker M, Sankoff D (1984) RNA secondary structures and their prediction. B Math Biol 46:591-621.
28. Maurer SB (2003) Directed acyclic graphs. Handbook of Graph Theory, eds JL Gross and J Yellen (CRC, Boca Raton, FL), pp 142-155.
29. Leontis NB, Westhof E (1998) The 5S rRNA loop E: Chemical probing and phylogenetic data versus crystal structure. RNA 4:1134-1153. (Pubitemid 28413459)
30. Lemieux S, Chartrand P, Cedergren R, Major F (1998) Modeling active RNA structures using the intersection of conformational space: Application to the lead-activated ribozyme. RNA 4:739-749. (Pubitemid 28317823)
31. Harris S, Schroeder SJ (2010) Nuclear magnetic resonance structure of the prohead RNA E-loop hairpin. Biochemistry 49:5989-5997.
32. Cate JH, et al. (1996) Crystal structure of a group I ribozyme domain: principles of RNA packing. Science 273:1678-1685. (Pubitemid 26317777)
33. Ye JD, et al. (2008) Synthetic antibodies for specific recognition and crystallization of structured RNA. Proc Natl Acad Sci USA 105:82-87.
34. Stombaugh J, Zirbel CL,Westhof E, Leontis NB (2009) Frequency and isostericity of RNA base pairs. Nucleic Acids Res 37:2294-2312.
35. Sarver M, Zirbel C, Stombaugh J, Mokdad A, Leontis N (2008) FR3D: Finding local and composite recurrent structural motifs in RNA 3D structures. J Math Biol 56:215-252. (Pubitemid 350172192)
36. Tijerina P, Mohr S, Russell R (2007) DMS footprinting of structured RNAs and RNA-protein complexes. Nat Protoc 2:2608-2623.
37. Stern S, Moazed D, Noller HF (1988) Structural analysis of RNA using chemical and enzymatic probing monitored by primer extension. Methods Enzymol 164:481-489. (Pubitemid 19067612)
38. Beauchamp K, Sripakdeevong P, Das R (2011) Why can't we predict RNA structure at atomic resolution? RNA 3D Structure Analysis and Prediction, eds N Leontis and E Westhof (Springer), in-press.
39. Mandell DJ, Coutsias EA, Kortemme T (2009) Subangstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling. Nat Methods 6:551-552.
40. Rohl CA, Strauss CEM, Misura K, Baker D (2004) Protein structure prediction using Rosetta. Methods Enzymol 66-93. (Pubitemid 38401787)
41. Sato T, Tsuneda T, Hirao K (2005) A density-functional study on pi-aromatic interaction: Benzene dimer and naphthalene dimer. J Chem Phys 123:104307-1-104307-10.
42. Ponder JW, et al. (2010) Current status of the AMOEBA polarizable force field. J Phys Chem B 114:2549-2564.
43. Shen Y, et al. (2008) Consistent blind protein structure generation from NMR chemical shift data. Proc Natl Acad Sci USA 105:4685-4690. (Pubitemid 351753807)
44. Vallurupalli P, Hansen DF, Kay LE (2008) Structures of invisible, excited protein states by relaxation dispersion NMR spectroscopy. Proc Natl Acad Sci USA 105:11766-11771.
45. Zuo X, et al. (2010) Solution structure of the cap-independent translational enhancer and ribosome-binding element in the 3′ UTR of turnip crinkle virus. Proc Natl Acad Sci USA 107:1385-1390.
46. Kladwang W, Cordero P, Das R (2011) A mutate-and-map strategy accurately infers the base pairs of a 35-nucleotide model RNA. RNA 17:522-534.