Pathway modulation, circular permutation and rapid RNA folding under kinetic control

Journal of Molecular Biology

Volumn 286, Issue 3, 1999, Pages 721-731

  Pan, Tao ^a   Fang, Xingwang ^a   Sosnick, Tobin ^a  

^a UNIVERSITY OF CHICAGO   (United States)

Author keywords

Circular permutation; Folding pathway; Kinetic control; Ribozyme; RNA folding

Indexed keywords

MAGNESIUM ION; RIBONUCLEASE P; RIBOZYME;

ARTICLE; BACILLUS SUBTILIS; CATALYSIS; KINETICS; MOLECULAR INTERACTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN FOLDING; RNA STRUCTURE; SPECTROSCOPY; THERMODYNAMICS;

BACILLUS SUBTILIS; POSIBACTERIA;

EID: 0033605081     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.2516     Document Type: Article

References (29)

1. Altman S., Kirsebom L., Talbot S. Recent studies of ribonuclease P. FASEB J. 7:1993;7-14.
2. Baldwin R. L. On-pathway versus off-pathway folding intermediates. Folding Des. 1:1996;R1-8.
3. Banerjee A. R., Jaeger J. A., Turner D. H. Thermal unfolding of a group I ribozyme: the low-temperature transition is primarily disruption of tertiary structure. Biochemistry. 32:1993;153-163.
4. Celander D. W., Cech T. R. Visualizing the higher order folding of a catalytic RNA molecule. Science. 251:1991;401-407.
5. Cole P. E., Crothers D. M. Conformational changes of transfer ribonucleic acid. Relaxation kinetics of the early melting transition of methionine transfer ribonucleic acid (Escherichia coli). Biochemistry. 11:1972;4368-4374.
6. Crothers D. M., Cole P. E., Hilbers C. W., Shulman R. G. The molecular mechanism of thermal unfolding of Escherichia coli formylmethionine transfer RNA. J. Mol. Biol. 87:1974;63-88.
7. Doherty E. A., Doudna J. A. The P4-P6 domain directs higher order folding of the Tetrahymena ribozyme core. Biochemistry. 36:1997;3159-3169.
8. Harris M. E., Nolan J. M., Malhotra A., Brown J. W., Pace N. R. Global architecture of the ribonuclease P RNA-pre tRNA complex. EMBO J. 13:1994;3953-3963.
9. Kurz J. C., Niranjanakumari S., Fierke C. A. Protein component of Bacillus subtilis RNase P specifically enhances the affinity for precursor-tRNAAsp. Biochemistry. 37:1998;2393-2400.
10. Laing L. G., Draper D. E. Thermodynamics of RNA folding in a conserved ribosomal RNA domain. J. Mol. Biol. 237:1994;560-576.
11. Loria A., Pan T. Domain structure of the ribozyme from eubacterial ribonuclease P. RNA. 2:1996;551-563.
12. Loria A., Pan T. Recognition of the T stem-loop of a pre-tRNA substrate by the ribozyme from Bacillus subtilis ribonuclease P. Biochemistry. 36:1997;6317-6325.
13. Milligan J. F., Uhlenbeck O. C. Synthesis of small RNAs using T7 RNA polymerase. Methods Enzymol. 180:1989;51-62.
14. Murphy F. L., Cech T. R. An independently folding domain of RNA tertiary structure within the Tetrahymena ribozyme. Biochemistry. 32:1993;5291-5300.
15. Odell L., Huang V., Jakacka M., Pan T. Interaction of structural modules in substrate binding by the ribozyme from Bacillus subtilis RNase P. Nucl. Acids Res. 26:1998;3717-3723.
16. Pace N. R., Brown J. W. Evolutionary perspective on the structure and function of ribonuclease P, a ribozyme. J. Bacteriol. 177:1995;1919-1928.
17. Pan J., Thirumalai D., Woodson S. A. Folding of RNA involves parallel pathways. J. Mol. Biol. 273:1997;7-13.
18. Pan T. Higher order folding and domain analysis of the ribozyme from Bacillus subtilis ribonuclease P. Biochemistry. 34:1995;902-909.
19. Pan T., Jakacka M. Multiple substrate binding sites in the ribozyme from Bacillus subtilis RNase P. EMBO. J. 15:1996;2249-2255.
20. Pan T., Sosnick T. R. Intermediates and kinetic traps in the folding of a large ribozyme revealed by circular dichroism and UV absorbance spectroscopies and catalytic activity. Nature Struct. Biol. 4:1997;931-938.
21. Pan T., Zhong K. Selection of circularly permuted ribozymes from Bacillus subtilis RNAse P by substrate binding. Biochemistry. 33:1994;14207-14212.
22. Pan T., Loria A., Zhong K. Probing of tertiary interactions in RNA: 2′-hydroxyl-base contacts between the RNase P RNA and pre-tRNA. Proc. Natl Acad. Sci. USA. 92:1995;12510-12514.
23. Sclavi B., Sullivan M., Chance M. R., Brenowitz M., Woodson S. A. RNA folding at millisecond intervals by synchrotron hydroxyl radical footprinting. Science. 279:1998;1940-1943.
24. Treiber D. K., Rook M. S., Zarrinkar P. P., Williamson J. R. Kinetic intermediates trapped by native interactions in RNA folding. Science. 279:1998;1943-1946.
25. Phe(yeast): kinetics and electrostatic repulsion. Eur. J. Biochem. 55:1975;439-444.
26. Viguera A. R., Serrano L., Wilmanns M. Different folding transition states may result in the same native structure. Nature Struct. Biol. 3:1996;874-880.
27. Westhof E., Wesolowski D., Altman S. Mapping in three dimensions of regions in a catalytic RNA protected from attack by an Fe(II)-EDTA reagent. J. Mol. Biol. 258:1996;600-613.
28. Zarrinkar P. P., Williamson J. R. Kinetic intermediates in RNA folding. Science. 265:1994;918-924.
29. Zarrinkar P. P., Wang J., Williamson J. R. Slow folding kinetics of RNase P RNA. RNA. 2:1996;564-573.