Concerted folding of a Candida ribozyme into the catalytically active structure posterior to a rapid RNA compaction

Nucleic Acids Research

Volumn 31, Issue 14, 2003, Pages 3901-3908

  Xiao, Mu ^c   Leibowitz, Michael J ^a,b   Zhang, Yi ^c  

^a RUTGERS ROBERT WOOD JOHNSON MEDICAL SCHOOL   (United States)

^b RUTGERS CANCER INSTITUTE OF NEW JERSEY   (United States)

^c WUHAN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

MAGNESIUM ION; RIBONUCLEASE T1; RIBOZYME; RNA; FUNGAL RNA; MAGNESIUM;

ARTICLE; CANDIDA ALBICANS; CATALYSIS; CHEMICAL BINDING; CHEMICAL REACTION KINETICS; CONCENTRATION (PARAMETERS); CONTROLLED STUDY; INTRON; MOLECULAR MODEL; NONHUMAN; PRIORITY JOURNAL; RNA CLEAVAGE; RNA CONFORMATION; RNA STRUCTURE; STRUCTURE ANALYSIS; CHEMISTRY; CONFORMATION; DOSE RESPONSE; DRUG EFFECT; ENZYME SPECIFICITY; ENZYMOLOGY; GENETICS; KINETICS; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE;

CANDIDA; CANDIDA ALBICANS; KOBUS; TETRAHYMENA;

BASE SEQUENCE; CANDIDA ALBICANS; CATALYSIS; DOSE-RESPONSE RELATIONSHIP, DRUG; KINETICS; MAGNESIUM; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RNA, CATALYTIC; RNA, FUNGAL; SUBSTRATE SPECIFICITY;

EID: 0242317691     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg455     Document Type: Article

References (30)

1. Doudna,J.A. and Cech,T.R. (2002) The chemical repertoire of natural ribozymes. Nature, 418, 222-228.
2. Narlikar,G.J. and Herschlag,D. (1997) Mechanistic aspects of enzymatic catalysis: lessons from comparison of RNA and protein enzymes. Annu. Rev. Biochem., 66, 19-59.
3. Thirumalai,D., Lee,N., Woodson,S.A. and Klimov,D.K. (2001) Early events in RNA folding. Annu. Rev. Phys. Chem., 52, 751-762.
4. Cech,T.R. (1990) Self-splicing of group I introns. Annu. Rev. Biochem., 59, 543-568.
5. von Ahsen,U., Davies,J. and Schroeder,R. (1991) Antibiotic inhibition of group I ribozyme function. Nature, 353, 368-370.
6. Weeks,K.M. and Cech,T.R. (1995) Protein facilitation of group I splicing by assembly of the catalytic core and the 5-prime splice site domain. Cell, 82, 221-230.
7. van der Horst,G. and Tabak,H.F. (1985) Self-splicing of yeast mitochondrial ribosomal and messenger RNA precursors. Cell, 40, 759-766.
8. Mercure,S., Montplaisir,S. and Lemay,G. (1993) Correlation between the presence of a self-splicing intron in the 25S rDNA of Calbicans and strains susceptibility to 5-fluorocytosine. Nucleic Acids Res., 21, 6020-6027.
9. Michel,F. and Westhof,E. (1990) Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J. Mol. Biol., 216, 585-610.
10. Caprara,M.G., Lehnert,V., Lambowitz,A.M. and Westhof,E. (1996) A tyrosyl-tRNA synthetase recognizes a conserved tRNA-like structural motif in the group I intron catalytic core. Cell, 87, 1135-1145.
11. Caprara,M.G., Mohr,G. and Lambowitz,A.M. (1996) A tyrosyl-tRNA synthetase protein induces tertiary folding of the group I intron catalytic core. J. Mol. Biol., 257, 512-531.
12. Buchmueller,K., Webb,A.E., Richardson,D.A. and Weeks,K.M. (2000) A collapsed non-native RNA folding state. Nature Struct. Biol., 7, 362-366.
13. Webb,A.E. and Weeks,K.M. (2001) A collapsed state functions to self-chaperone RNA folding into a native ribonucleoprotein complex. Nature Struct. Biol., 8, 135-140.
14. Treiber,D.K. and Williamson,J.R. (2001) Beyond kinetic traps in RNA folding. Curr. Opin. Struct. Biol., 11, 309-314.
15. Celander,D.W. and Cech,T.R. (1991) Visualizing the higher order folding of a catalytic RNA molecule. Science, 251, 401-407.
16. Sclavi,B., Sullivan,M., Chance,M.R., Brenowitz,M. and Woodson,S.A. (1998) RNA folding at millisecond intervals by synchrotron hydroxyl radical footprinting. Science, 279, 1940-1943.
17. Pan,J., Thirumalai,D. and Woodson,S.A. (1999) Magnesium-dependent folding of self-splicing RNA: exploring the link between cooperativity, thermodynamics and kinetics. Proc. Natl Acad. Sci. USA, 96, 6149-6154.
18. Zhuang,X.W., Bartley,L.E., Babcock,H.P., Russell,R., Ha,T., Herschlag,D. and Chu,S. (2000) A single-molecule study of RNA catalysis and folding. Science, 288, 2048-2051.
19. Pan,J., Thirumalai,D. and Woodson,S.A. (1997) Folding of RNA involves parallel pathways. J. Mol. Biol., 273, 7-13.
20. 2+ concentration for kinetic folding of the Tetrahymena ribozyme. Proc. Natl Acad. Sci. USA, 96, 12471-12476.
21. Russell,R. and Herschlag,D. (1999) New pathways in folding of the Tetrahymena group I RNA enzyme. J. Mol. Biol., 291, 1155-1167.
22. Treiber,D.K., Rook,M.S., Zarrinkar,P.P. and Williamson,J.R. (1998) Kinetic intermediates trapped by native interactions in RNA folding. Science, 279, 1943-1946.
23. Pan,J., Deras,M.L. and Woodson,S.A. (2000) Fast folding of a ribozyme by stabilizing core interactions: evidence for multiple folding pathways in RNA. J. Mol. Biol., 296, 133-144.
24. Treiber,D.K. and Williamson,J.R. (2001) Concerted kinetic folding of a multidomain ribozyme with a disrupted loop-receptor interaction. J. Mol. Biol., 305, 11-21.
25. 2+-dependent folding of a large ribozyme without kinetic traps. Nature Struct. Biol., 6, 1091-1095.
26. Zhang,Y. and Leibowitz,M.J. (2001) Folding of the group I intron ribozyme from the 26S rRNA gene of Candida albicans. Nucleic Acids Res., 29, 2644-2653.
27. Zhang,Y., Li,Z.J., Pilch,D.S. and Leibowitz,M.J. (2002) Pentamidine inhibits catalytic activity of group I intron Ca.LSU by altering RNA folding. Nucleic Acids Res., 30, 2961-2971.
28. Russell,R., Millett,L.S., Tate,M.W., Kwok,L.W., Nakatani,B., Gruner,S.M., Mochrie,V.P., Dniach,S., Hersehlag,D. and Pollack,L. (2002) Rapid compaction during RNA folding. Proc. Natl Acad Sci. USA, 99, 4266-4271.
29. Rangan,P., Masquida,B., Westhof,E. and Woodson,S.A. (2003) Assembly of core helices and rapid tertiary folding of a small bacterial group I ribozyme. Proc. Natl Acad. Sci. USA, 100, 1574-1579.
30. Pan,J. and Woodson,S.A. (1998) Folding intermediates of a self-splicing RNA: mispairing of the catalytic core. J. Mol. Biol., 280, 597-609.