RNA backbone: Consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution)

RNA

Volumn 14, Issue 3, 2008, Pages 465-481

  Richardson, Jane S ^a   Schneider, Bohdan ^b   Murray, Laura W ^a   Kapral, Gary J ^a   Immormino, Robert M ^a   Headd, Jeffrey J ^a   Richardson, David C ^a   Ham, Daniela ^b   Hershkovits, Eli ^c   Williams, Loren Dean ^d   Keating, Kevin S ^e   Pyle, Anna Marie ^e   Micallef, David ^f   Westbrook, John ^f   Berman, Helen M ^f  

^a DUKE UNIVERSITY MEDICAL CENTER   (United States)

^b INSTITUTE OF MATHEMATICS   (Czech Republic)

^c GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

^d GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

^e YALE UNIVERSITY   (United States)

^f RUTGERS UNIVERSITY   (United States)

Author keywords

Conformational strings; Multidimensional data analysis; RNA backbone conformation; RNA backbone torsion angles; RNA structural motifs; Structural bioinformatics

Indexed keywords

NUCLEOTIDE; RNA;

ARTICLE; BIOINFORMATICS; CLUSTER ANALYSIS; CONSENSUS; CRYSTALLOGRAPHY; DATA ANALYSIS; GENE CLUSTER; HYDROGEN BOND; NOMENCLATURE; PRIORITY JOURNAL; RNA STRUCTURE; TORSION; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; CONSENSUS SEQUENCE;

COMPUTATIONAL BIOLOGY; CONSENSUS SEQUENCE; MODELS, MOLECULAR; MOLECULAR STRUCTURE; NUCLEIC ACID CONFORMATION; RNA; TERMINOLOGY AS TOPIC;

EID: 40449091092     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.657708     Document Type: Article

References (55)

1. Adams, P.L., Stahley, M.R., Kosek, A.B., Wang, J., and Strobel, S.A. 2004. Crystal structure of a self-splicing group I intron with both exons. Nature 430: 45-50.
2. Altona, C. and Sundaralingam, M. 1972. Conformational analysis of the sugar ring in nucleosides and nucleotides. A new description using the concept of pseudorotation. J. Am. Chem. Soc. 94: 8205.
3. 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 Å resolution. Science 289: 905-920.
4. Berman, H.M., Olson, W.K., Beveridge, D.L., Westbrook, J., Gelbin, A., Demeny, T., Hsieh, S.H., Srinivasan, A.R., and Schneider, B. 1992. The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids. Biophys. J. 63: 751-759.
5. 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. doi: 10.1093/nar/28.1.235.
6. Brameld, K.A. and Goddard, W.A. 1999. Ab initio quantum mechanical study of the structures and energies for the pseudorotation of 5′ dehydroxy analogues of 2′ deoxyribose and ribose sugars. J. Am. Chem. Soc. 121: 985-993.
7. Cheong, C., Varani, G., and Tinoco Jr., I. 1991. Structure of an unusually stable RNA hairpin, 5′GGAC(UUCG)GUCC. Nature 346: 680-682.
8. Correll, C.C., Freeborn, B., Moore, P.B., and Steitz, T.A. 1997. Metals, motifs, and recognition in the crystal structure of a 5S rRNA domain. Cell 91: 705-712.
9. Correll, C.C., Beneken, J., Plantinga, M.J., Lubbers, M., and Chan, Y.L. 2003. The common and distinctive features of the bulged-G motif based on a 1.04 Å resolution RNA structure. Nucleic Acids Res. 31: 6806-6818.
10. Cremer, D. and Pople, J.A. 1975. General definition of ring puckering coordinates. J. Am. Chem. Soc. 97: 1354-1358.
11. Davis, I.W., Leaver-Fay, A., Chen, V.B., Block, J.N., Kapral, G.J., Wang, X., Murray, L.W., Arendall III, W.B., Snoeyink, J., Richardson, J.S., et al. 2007. MolProbity: All-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res. 35: W375-W383. doi: 10.1093/nar/gkm216.
12. Duarte, C.M. and Pyle, A.M. 1998. Stepping through an RNA structure: A novel approach to conformational analysis. J. Mol. Biol. 284: 1465-1478.
13. Dunbrack, R.L. and Cohen, F.E. 1997. Bayesian statistical analysis of protein side-chain rotamer preferences. Protein Sci. 6: 1661-1681.
14. Ennifar, E., Nikouline, A., Tishchenko, S., Serganov, A., Nevskaya, N., Garber, M., Ehresmann, B., Ehresmann, C., Nikonov, S., and Dumas, P. 2000. The crystal structure of UUCG tetraloop. J. Mol. Biol. 304: 35-42.
15. Ferre-D'Amaré, A.R., Zhou, K., and Doudna, J.A. 1998. Crystal structure of a hepatitis delta virus ribozyme. Nature 395: 567-574.
16. Gelbin, A., Schneider, B., Clowney, L., Hsieh, S.-H., Olson, W.K., and Berman, H.M. 1996. Geometric parameters in nucleic acids: Sugar and phosphate constituents. J. Am. Chem. Soc. 118: 519-528.
17. Gielis, J. 2003. Inventing the circle: The geometry of nature. Geniaal Press. Antwerp, Belgium.
18. Golden, B.L., Kim, H., and Chase, E. 2005. Crystal structure of a phage Twort group I ribozyme-product complex. Nat. Struct. Mol. Biol. 12: 82-89.
19. Gridgeman, N.T. 1970. Lamé ovals. Math. Gaz. 54: 31-37.
20. Hamma, T. and Ferre-D'Amaré, A. 2004. Structure of protein L7Ae bound to a K-turn derived from an archaeal box H/ACA sRNA at 1.8 Å resolution. Structure 12: 893-903.
21. 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 Hm LSU 23S rRNA. Nucleic Acids Res. 31: 6249-6257. doi: 10.1093/nar/gkg835.
22. 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.
23. Hsiao, C., Mohan, S., Hershkovitz, E., Tannenbaum, A., and Williams, L.D. 2006. Single nucleotide choreography. Nucleic Acids Res. 34: 1481-1491. doi: 10.1093/nar/gkj500.
24. Inselberg, A. 2007. Parallel coordinates. Springer, New York.
25. Ippolito, J.A. and Steitz, T.A. 2000. The structure of the HIV-1 RRE high affinity rev binding site at 1.6 Å resolution. J. Mol. Biol. 295: 711-717.
26. Jang, S.B., Baeyens, K., Jeong, M.S., Santalucia Jr., J., Turner, D., and Holbrook, S.R. 2004. Structures of two RNA octamers containing tandem G•A base pairs. Acta Crystallogr. D60: 829-835.
27. Kacer, V., Scaringe, S.A., Scarsdale, J.N., and Rife, J.P. 2003. Crystal structures of r(GGUCACAGCCC)2. Acta Crystallogr. D59: 423-432.
28. Kleywegt, G.J. and Jones, T.A. 1994. A super position. CCP4/ESFEACBM Newsletter Protein Crystallogr 31: 9-14.
29. Kim, S.-H., Berman, H.M., Newton, M.D., and Seeman, N.C. 1973. Seven basic conformations of nucleic acid structural units. Acta Crystallogr. B29: 703-710.
30. Leontis, N.B. and Westhof, E. 1998. A common motif organizes the structure of multi-helix loops in 16S and 23S ribosomal RNAs. J. Mol. Biol. 283: 571-583.
31. Leontis, N.B. and Westhof, E. 2001. Geometric nomeclature and classification of RNA base pairs. RNA 7: 499-512.
32. Leontis, N.B., Altman, R.B., Berman, H.M., Brenner, S.E., Brown, J.W., Engelke, D.R., Harvey, S.C., Holbrook, S.R., Jossinet, F., Lewis, S.E., et al. 2006. The RNA Ontology Consortium: An open invitation to the RNA community. RNA 12: 533-541.
33. Lovell, S.C., Word, J.M., Richardson, J.S., and Richardson, D.C. 2000. The penultimate rotamer library. Proteins 40: 389-408.
34. Malathi, R. and Yathindra, N. 1980. A novel virtual bond scheme to probe ordered and random coil conformations of nucleic acids: Configurational statistics of polynucleotide chains. Curr. Sci. 49: 803-807.
35. Murray, L.W., Arendall III, W.B., Richardson, D.C., and Richardson, J.S. 2003. RNA backbone is rotameric. Proc. Natl. Acad. Sci. 100: 13904-13909.
36. Murray, L.J., Richardson, J.S., Arendall, W.B., and Richardson, D.C. 2005. RNA backbone rotamers - Finding your way in 7 dimensions. Biochem. Soc. Trans. 33: 485-487.
37. Murthy, V.L., Srinivasan, R., Draper, D.E., and Rose, G.D. 1999. RNABase: An annotated database of RNA structures. J. Mol. Biol. 291: 313-327.
38. Olson, W.K. 1980. Configurational statistics of polynucleotide chains. An updated virtual bond model to treat effects of base stacking. Macromolecules 13: 721-728.
39. Olson, W.K. 1982. How flexible is the furanose ring? 2. An updated potential energy estimate. J. Am. Chem. Soc. 104: 278-286.
40. +(anti) mispairs. Biochemistry 38: 2826-2831.
41. Parkinson, G., Vojtechovsky, J., Clowney, L., Bruenger, A.T., and Berman, H.M. 1996. New parameters for the refinement of nucleic acid containing structures. Acta Crystallogr. D52: 57-64.
42. Richardson, D.C. and Richardson, J.S. 1992. The kinemage: A tool for scientific illustration. Protein Sci. 1: 3-9.
43. Richardson, J.S. and Richardson, D.C. 2001. MAGE, PROBE, and Kinemages. In International tables for crystallography (eds. M.G. Rossmann and E. Arnold), Vol. F, pp. 727-730. Kluwer Academic Publishers, Dordrecht, The Netherlands.
44. Rubin, J., Brennan, T., and Sundaralingam, M. 1972. Crystal and molecular structure of naturally occurring dinucleoside monophosphate uridylyl-(3′,5′)-adenosine hemihydrate. Conformational rigidity of the nucleotide unit and models for polynucleotide chain folding. Biochemistry 11: 3112-3118.
45. Sarver, M., Zirbel, C.L., Stombaugh, J., Mokdad, A., and Leontis, N.B. 2007. FR3D: Finding local and composite recurrent structural motifs in RNA 3D structures. J. Math. Biol. 56: 215-252.
46. Schluenzen, F., Tocilj, A., Zarivach, R., Harms, J., Gluehmann, M., Janell, D., Bashan, A., Bartels, H., Agmon, I., Franceschi, F., et al. 2000. Structure of functionally activated small ribosomal subunit at 3.3 Å resolution. Cell 102: 615-623.
47. Schneider, B., Moravek, Z., and Berman, H.M. 2004. RNA conformational classes. Nucleic Acids Res. 32: 1666-1677. doi: 10.1093/nar/gkh333.
48. Schultes, E., Hraber, P.T., and LaBean, T.H. 1999. A parametrization of RNA sequence space. Complexity 4: 61-71.
49. Shi, H. and Moore, P.B. 2000. The crystal structure of yeast phenylalanine tRNA at 1.93 Å resolution: A classic structure revisited. RNA 6: 1091-1105.
50. Sims, G.E. and Kim, S.H. 2003. Global mapping of nucleic acid conformational space: Dinucleoside monophosphate conformations and transition pathways among conformational classes. Nucleic Acids Res. 31: 5607-5616. doi: 10.1093/nar/gkg750.
51. Sussman, J.L., Seeman, N.C., Kim, S.-H., and Berman, H.M. 1972. The crystal structure of a naturally occurring dinucleotide phosphate uridylyl 3′,5′-adenosine phosphate. Models for RNA chain folding. J. Mol. Biol. 66: 403-421.
52. Wadley, L.M. and Pyle, A.M. 2004. The identification of novel RNA structural motifs using COMPADRES: An automated approach to structural discovery. Nucleic Acids Res. 32: 6650-6659. doi: 10.1093/nar/gkh1002.
53. Wimberley, B.T., Broderson, D.E., Clemons, W.M., Morgan-Warren, R.J., Carter, A.P., Vonrhein, C., Hartsch, T., and Ramakrishnan, V. 2000. Structure of the 30S ribosomal subunit. Nature 407: 327-339.
54. Woese, C.R., Winker, S., and Gutell, R.R. 1990. Architecture of ribosomal RNA - Constraints on the sequence of tetraloops. Proc. Natl. Acad. Sci. 87: 8467-8471.
55. Word, J.M., Lovell, S.C., LaBean, T.H., Taylor, H.C., Zalis, M.E., Presley, B.K., Richardson, J.S., and Richardson, D.C. 1999. Visualizing and quantifying molecular goodness-of-fit: Small-probe contact dots with explicit hydrogens. J. Mol. Biol. 285: 1711-1733.