Developing three-dimensional models of putative-folding intermediates of the HDV ribozyme

Structure

Volumn 18, Issue 12, 2010, Pages 1608-1616

  Reymond, Cédric ^a   Lévesque, Dominique ^a   Bisaillon, Martin ^a   Perreault, Jean Pierre ^a  

^a UNIVERSITÉ DE SHERBROOKE   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

RIBOZYME; RNA;

ACYLATION; ARTICLE; CATALYSIS; COMPUTER PROGRAM; ENZYME STRUCTURE; HEPATITIS DELTA VIRUS; NONHUMAN; PRIORITY JOURNAL; PROTEIN STRUCTURE; RNA STRUCTURE; RNA SYNTHESIS;

BASE SEQUENCE; CATALYSIS; COMPUTATIONAL BIOLOGY; HEPATITIS DELTA VIRUS; MODELS, BIOLOGICAL; MODELS, MOLECULAR; MOLECULAR CONFORMATION; NUCLEIC ACID CONFORMATION; RNA, CATALYTIC; VALIDATION STUDIES AS TOPIC;

HEPATITIS DELTA VIRUS;

EID: 78649781975     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2010.09.024     Document Type: Article

References (28)

1. N.J. Baird, E. Westhof, H. Qin, T. Pan, and T.R. Sosnick Structure of a folding intermediate reveals the interplay between core and peripheral elements in RNA folding J. Mol. Biol. 352 2005 712 722
2. M.D. Been HDV ribozymes Curr. Top. Microbiol. Immunol. 307 2006 47 65
3. S. Chauhan, and S.A. Woodson Tertiary interactions determine the accuracy of RNA folding J. Am. Chem. Soc. 130 2008 1296 1303
4. J.C. Cochrane, and S.A. Strobel Catalytic strategies of self-cleaving ribozymes Acc. Chem. Res. 41 2008 1027 1035
5. J.A. Cruz, and E. Westhof The dynamic landscapes of RNA architecture Cell 136 2009 604 609
6. R. Das, and D. Baker Automated de novo prediction of native-like RNA tertiary structures Proc. Natl. Acad. Sci. USA 104 2007 14664 14669
7. P. Deschênes, J. Ouellet, J. Perreault, and J.P. Perreault Formation of the P1.1 pseudoknot is critical for both the cleavage activity and substrate specificity of an antigenomic trans-acting hepatitis delta ribozyme Nucleic Acids Res. 31 2003 2087 2096
8. F. Ding, S. Sharma, P. Chalasani, V.V. Demidov, N.E. Broude, and N.V. Dokholyan Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms RNA 14 2008 1164 1173
9. A.R. Ferré-D'Amaré, K. Zhou, and J.A. Doudna Crystal structure of a hepatitis delta virus ribozyme Nature 395 1998 567 574
10. J.L. Fiore, B. Kraemer, F. Koberling, R. Edmann, and D.J. Nesbitt Enthalpy-driven RNA folding: single-molecule thermodynamics of tetraloop receptor tertiary interaction Biochemistry 48 2009 2550 2558
11. W.J. Greenleaf, K.L. Frieda, D.A. Foster, M.T. Woodside, and S.M. Block Direct observation of hierarchical folding in single riboswitch aptamers Science 319 2008 630 633
12. W. Humphrey, A. Dalke, and K. Schulten VMD: visual molecular dynamics J. Mol. Graph. 14 1996 33 38
13. A. Ke, K. Zhou, F. Ding, J.H. Cate, and J.A. Doudna A conformational switch controls hepatitis delta virus ribozyme catalysis Nature 429 2004 201 205
14. A. Laederach, R. Das, Q. Vicens, S.M. Pearlman, M. Brenowitz, D. Herschlag, and R.B. Altman Semiautomated and rapid quantification of nucleic acid footprinting and structure mapping experiments Nat. Protoc. 3 2008 1395 1401
15. D.M. Lilley Structure, folding and mechanisms of ribozymes Curr. Opin. Struct. Biol. 15 2005 313 323
16. E.M. Moody, and P.C. Bevilacqua Folding of a stable DNA motif involves a highly cooperative network of interactions J. Am. Chem. Soc. 125 2003 16285 16293
17. S.A. Mortimer, and K.M. Weeks Time-resolved RNA SHAPE chemistry J. Am. Chem. Soc. 130 2008 16178 16180
18. A. Nehdi, J. Perreault, J.D. Beaudoin, and J.P. Perreault A novel structural rearrangement of hepatitis delta virus antigenomic ribozyme Nucleic Acids Res. 35 2007 6820 6831
19. F. Nishikawa, and S. Nishikawa Requirement for canonical base pairing in the short pseudoknot structure of genomic hepatitis delta virus ribozyme Nucleic Acids Res. 28 2000 925 931
20. B. Onoa, and I. Tinoco Jr. RNA folding and unfolding Curr. Opin. Struct. Biol. 14 2004 374 379
21. J. Ouellet, and J.P. Perreault Cross-linking experiments reveal the presence of novel structural features between a hepatitis delta virus ribozyme and its substrate RNA 10 2004 1059 1072
22. M. Parisien, and F. Major The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data Nature 452 2008 51 55
23. C. Reymond, J. Ouellet, M. Bisaillon, and J.P. Perreault Examination of the folding pathway of the antigenomic hepatitis delta virus ribozyme reveals key interactions of the L3 loop RNA 13 2007 44 54
24. C. Reymond, M. Bisaillon, and J.P. Perreault Monitoring of an RNA multistep folding pathway by isothermal titration calorimetry Biophys. J. 96 2009 132 140
25. B.A. Shapiro, Y.G. Yingling, W. Kasprzak, and E. Bindewald Bridging the gap in RNA structure prediction Curr. Opin. Struct. Biol. 17 2007 157 165
26. T.R. Sosnick, and T. Pan Reduced contact order and RNA folding rates J. Mol. Biol. 342 2004 1359 1365
27. J.M. Watts, K.K. Dang, R.J. Gorelick, C.W. Leonard, J.W. Bess Jr., R. Swanstrom, C.L. Burch, and K.M. Weeks Architecture and secondary structure of an entire HIV-1 RNA genome Nature 460 2009 711 716
28. Z. Zhuang, L. Jaeger, and J.E. Shea Probing the structural hierarchy and energy landscape of an RNA T-loop harpin Nucleic Acids Res. 35 2007 6995 7002