The identification of novel RNA structural motifs using COMPADRES: An automated approach to structural discovery

Nucleic Acids Research

Volumn 32, Issue 22, 2004, Pages 6650-6659

  Wadley, Leven M ^c   Pyle, Anna Marie ^a,b  

^a YALE UNIVERSITY   (United States)

^b HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^c Columbia University ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE; AMINO ACID; RNA;

ALGORITHM; AMINO ACID SEQUENCE; ANALYTIC METHOD; ARTICLE; AUTOANALYSIS; COMPUTER PROGRAM; CONTROLLED STUDY; CORRELATION ANALYSIS; HALOARCULA MARISMORTUI; MOLECULAR INTERACTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN MOTIF; PROTEIN SECONDARY STRUCTURE; RNA STRUCTURE; STRUCTURE ANALYSIS;

ADENOSINE; ALGORITHMS; HYDROGEN BONDING; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; RNA; SOFTWARE;

EID: 13544255744     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh1002     Document Type: Article

References (53)

1. Cech,T.R. (2002) Ribozymes, the first 20 years. Biochem. Soc. Trans., 30, 1162-1166.
2. Kim,S.H., Suddath,F.L., Quigley,G.J., McPherson,A., Sussman,J.L., Wang,A.H.J., Seeman,N.C. and Rich,A. (1974) Three-dimensional tertiary structure of yeast phenylalanine transfer RNA. Science, 185, 435-440.
3. Robertus,J.D., Ladner,J.E., Finch,J.T., Rhodes,D., Brown,R.S., Clark,B.F. and Klug,A. (1974) Structure of yeast phenylalanine tRNA at 3 Å resolution. Nature, 250, 546-551.
4. Ramakrishnan,V. (2002) Ribosome structure and the mechanism of translation. Cell, 108, 557-572.
5. Leontis,N.B. and Westhof,E. (2003) Analysis of RNA motifs. Curr. Opin. Struct. Biol., 13, 300-308.
6. Moore,P.B. (1999) Structural motifs in RNA. Annu. Rev. Biochem., 68, 287-300.
7. Nissen,P., Ippolito,J.A., Ban,N., Moore,P.B. and Steitz,T.A. (2001) RNA tertiary interactions in the large ribosomal subunit: the A-minor motif. Proc. Natl Acad. Sci. USA, 98, 4899-4903.
8. Cate,J.H., Gooding,A.R., Podell,E., Zhou,K., Golden,B.L., Kundrot,C.E., Cech,T.R. and Doudna,J.A. (1996) Crystal structure of a Group I ribozyme domain: principles of RNA packing. Science, 273 1678-1685.
9. Tamura,M. and Holbrook,S.R. (2002) Sequence and structural conservation in RNA ribose zippers. J. Mol. Biol., 320, 455-474.
10. Leontis,N.B. and Westhof,E. (2001) Geometric nomenclature and classification of RNA base pairs. RNA, 7, 499-512.
11. Leontis,N.B., Stombaugh,J. and Westhof,E. (2002) Motif prediction in ribosomal RNAs lessons and prospects for automated motif prediction in homologous RNA molecules. Biochimie, 84, 961-973.
12. Heus,H.A. and Pardi,A. (1991) Structural features that give rise to the unusual stability of RNA hairpins containing GNRA loops. Science, 253, 191-194.
13. Correll,C.C., Beneken,J., Plantinga,M.J., Lubbers,M. and Chan,Y.L. (2003) The common and the distinctive features of the bulged-G motif based on a 1.04 Å resolution RNA structure. Nucleic Acids Res., 31, 6806-6818.
14. Yang,X., Gerczei,T., Glover,L.T. and Correll,C.C. (2001) Crystal structures of restrictocin-inhibitor complexes with implications for RNA recognition and base flipping. Nature Struct. Biol., 8 968-973.
15. Duarte,C.M., Wadley,L.M. and Pyle,A.M. (2003) RNA structure comparison, motif search and discovery using a reduced representation of RNA conformational space. Nucleic Acids Res., 31, 4755-4761.
16. Klein,D.J., Schmeing,T.M., Moore,P.B. and Steitz,T.A. (2001) The Kink-turn: a new RNA secondary structure motif. EMBO J., 20 4214-4221.
17. Szep,S., Wang,J. and Moore,P.B. (2003) The crystal structure of a 26-nucleotide RNA containing a hook-turn. RNA, 9, 44-51.
18. Hershkovitz,E., Tannenbaum,E., Howerton,S.B., Sheth,A., Tannenbaum,A. and Williams,L.D. (2003) Automated identification of RNA conformational motifs: theory and application to the HM LSU 23S rRNA. Nucleic Acids Res., 31, 6249-6257.
19. Murray,L.J., Arendall,W.B.,III, Richardson,D.C. and Richardson,J.S. (2003) RNA backbone is rotameric. Proc. Natl Acad. Sci. USA, 100, 13904-13909.
20. Schneider,B., Moravek,Z. and Berman,H.M. (2004) RNA conformational classes. Nucleic Acids Res., 32, 1666-1677.
21. Olson,W.K. (1976) The spatial configuration of ordered polynucleotide chains. I. helix formation and base stacking. Biopolymers, 15, 859-878.
22. Malathi,R. and Yathindra,N. (1982) Secondary and tertiary structural foldings in tRNA. A diagonal plot analysis using the blocked nucleotide scheme. Biochem. J., 205, 457-460.
23. Duarte,C. and Pyle,A.M. (1998) Stepping through an RNA structure: a novel approach to conformational analysis. J. Mol. Biol. 284, 1465-1478.
24. Berman,H.M., Westbrook,J., Feng,Z., Gilliland,G., Bhat,T.N., Weissig,H., Shindyalov,I.N. and Bourne,P.E. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
25. Duarte,C.M. (2002) Computational approaches to the analysis and prediction of RNA structure. Ph.D. thesis, Columbia University, New York.
26. Saenger,W. (1984) Principles of Nucleic Acid Structure, 1st edn. Springer Verlag, New York.
27. Sussman,D., Nix,J.C. and Wilson,C. (2000) The structural basis for molecular recognition by the vitamin B 12 RNA aptamer. Nature Struct. Biol., 7, 53-57.
28. Juneau,K., Podell,E., Harrington,D.J. and Cech,T.R. (2001) Structural basis of the enhanced stability of a mutant ribozyme domain and a detailed view of RNA-solvent interactions. Structure (Camb. , 9, 221-231.
29. Leontis,N.B. and Westhof,E. (1998) A common motif organizes the structure of multi-helix loops in 16 S and 23 S ribosomal RNAs. J. Mol. Biol., 283, 571-583.
30. Harada,N., Maemura,K., Yamasaki,N. and Kimura,M. (1998) Identification by site-directed mutagenesis of amino acid residues in ribosomal protein L2 that are essential for binding to 23S ribosomal RNA. Biochim. Biophys. Acta, 1429, 176-186.
31. Diedrich,G., Spahn,C.M., Stelzl,U., Schafer,M.A., Wooten,T., Bochkariov,D.E., Cooperman,B.S., Traut,R.R. and Nierhaus,K.H. (2000) Ribosomal protein L2 is involved in the association of the ribosomal subunits, tRNA binding to A and P sites and peptidyl transfer. EMBO J. 19, 5241-5250.
32. Ogle,J.M., Murphy,F.V., Tarry,M.J. and Ramakrishnan,V. (2002) Selection of tRNA by the ribosome requires a transition from an open to a closed form. Cell, 111, 721-732.
33. Tereshko,V., Skripkin,E. and Patel,D.J. (2003) Encapsulating streptomycin within a small 40-mer RNA. Chem. Biol., 10, 175-187.
34. Serganov,A., Benard,L., Portier,C., Ennifar,E., Garber,M., Ehresmann,B. and Ehresmann,C. (2001) Role of conserved nucleotides in building the 16 S rRNA binding site for ribosomal protein S15. J. Mol. Biol., 305, 785-803.
35. Held,W.A., Ballou,B., Mizushima,S. and Nomura,M. (1974) Assembly mapping of 30 S ribosomal proteins from Escherichia coli. J. Biol. Chem., 249, 3103-3111.
36. Serganov,A., Polonskaia,A., Ehresmann,B., Ehresmann,C. and Patel,D.J. (2003) Ribosomal protein S15 represses its own translation via adaptation of an rRNA-like fold within its mRNA. EMBO J., 22, 1898-1908.
37. Klosterman,P.S., Hendrix,D.K., Tamura,M., Holbrook,S.R. and Brenner,S.E. (2004) Three-dimensional motifs from the SCOR, structural classification of RNA database: extruded strands, base triples, tetraloops and U-turns. Nucleic Acids Res., 32, 2342-2352.
38. Herold,M. and Nierhaus,K.H. (1987) Incorporation of six additional proteins to complete the assembly map of the 50 S subunit from Escherichia coli ribosomes. J. Biol. Chem., 262, 8826-8833.
39. Nomura,M. (1973) Assembly of bacterial ribosomes. Science 179, 864-873.
40. Held,W.A. and Nomura,M. (1973) Rate determining step in the reconstitution of Escherichia coli 30S ribosomal subunits. Biochemistry, 12, 3273-3281.
41. Nowotny,V. and Nierhaus,K.H. (1988) Assembly of the 30S subunit from Escherichia coli ribosomes occurs via two assembly domains which are initiated by S4 and S7. Biochemistry, 27, 7051-7055.
42. Ogle,J.M., Brodersen,D.E., Clemons,W.M.,Jr., Tarry,M.J., Carter,A.P. and Ramakrishnan,V. (2001) Recognition of cognate transfer RNA by the 30S ribosomal subunit. Science, 292, 897-902.
43. Culver,G.M. (2003) Assembly of the 30S ribosomal subunit. Biopolymers, 68, 234-249.
44. Krasilnikov,A.S., Xiao,Y., Pan,T. and Mondragon,A. (2004) Basis for structural diversity in homologous RNAs. Science, 306 104-107.
45. Matsumura,S., Ikawa,Y. and Inoue,J. (2003) Biochemical characterization of the kink-tum RNA motif. Nucleic Acids Res., 31, 5544-5551.
46. Portmann,S., Usman,N. and Egli,M. (1995) The crystal structure of r(CCCCGGGG) in two distinct lattices. Biochemistry, 34, 7569-7575.
47. Holm,L. and Sander,C. (1994) Searching protein structure databases has come of age. Proteins, 19, 165-173.
48. Orengo,C.A., Jones,D.T. and Thornton,J.M. (1994) Protein superfamilies and domain superfolds. Nature, 372, 631-634.
49. Orengo,C.A., Sillitoe,J., Reeves,G. and Pearl,F.M. (2001) Review: what can structural classifications reveal about protein evolution? J. Struct. Biol., 134, 145-165.
50. Mitchell,T. (1997) Machine Learning. McGraw-Hill, New York.
51. Carson,M. (1991) Ribbons 2.0. J. Appl. Cryst., 24 958-961.
52. Koradi,R., Billeter,M. and Wuthrich,K. (1996) MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graph., 14, 29-32, 51-55.
53. Cannone,J.J., Subramanian,S., Schnare,M.N., Collett,J.R., D'Souza,L.M., Du,Y., Feng,B., Lin,N., Madabusi,L.V., Muller,K.M. et al. (2002) The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics, 3, 2.