New pathways in folding of the Tetrahymena group I RNA enzyme

Journal of Molecular Biology

Volumn 291, Issue 5, 1999, Pages 1155-1167

  Russell, Rick ^a   Herschlag, Daniel ^a  

^a STANFORD UNIVERSITY   (United States)

Author keywords

Group I intron; Ribozyme; RNA folding; Tetrahymena thermophila

Indexed keywords

OLIGONUCLEOTIDE; RIBOZYME;

ARTICLE; CONTROLLED STUDY; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DEGRADATION; PROTEIN FOLDING; PROTEIN TERTIARY STRUCTURE; TETRAHYMENA;

PROTOZOA; TETRAHYMENA; TETRAHYMENA THERMOPHILA;

EID: 0033520410     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.3026     Document Type: Article

References (45)

1. Baldwin R. L. The nature of protein folding pathways: the classical versus the new view. J. Biomol. NMR. 5:1995;103-109.
2. 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.
3. Bevilacqua P. C., Kierzek R., Johnson K. A., Turner D. H. Dynamics of ribozyme binding of substrate revealed by fluorescence-detected stopped-flow methods. Science. 258:1992;1355-1358.
4. Brion P., Westhof E. Hierarchy and dynamics of RNA folding. Annu. Rev. Biophys. Biomol. Struct. 26:1997;113-137.
5. Cate J. H., Gooding A. R., Podell E., Zhou K., Golden B. L., Kundrot C. E., Cech T. R., Doudna J. A. Crystal structure of a group I ribozyme domain: principles of RNA packing. Science. 273:1996a;1678-1685.
6. Cate J. H., Gooding A. R., Podell E., Zhou K., Golden B. L., Szewczak A. A., Kundrot C. E., Cech T. R., Doudna J. A. RNA tertiary structure mediation by adenosine platforms. Science. 273:1996b;1696-1699.
7. Cate J. H., Hanna R. L., Doudna J. A. A magnesium ion core at the heart of a ribozyme domain. Nature Struct. Biol. 4:1997;553-558.
8. Cech T. R., Herschlag D. Group I ribozymes: substrate recognition, catalytic strategies, and comparative mechanistic analysis. Eckstein F., Lilley D. M. J. Catalytic RNA. 1997;1-17 Springer-Verlag, Berlin.
9. Cech T. R., Damberger S. H., Gutell R. R. Representation of the secondary and tertiary structure of group I introns. Nature Struct. Biol. 1:1994;273-280.
10. Celander D. W., Cech T. R. Visualizing the higher order folding of a catalytic RNA molecule. Science. 251:1991;401-407.
11. Dill K. A., Chan H. S. From Levinthal to pathways to funnels. Nature Struct. Biol. 4:1997;10-19.
12. Doherty E. A., Doudna J. A. The P4-P6 domain directs higher order folding of the Tetrahymena ribozyme core. Biochemistry. 36:1997;3159-3169.
13. Doherty E. A., Herschlag D., Doudna J. A. Assembly of an exceptionally stable RNA tertiary interface in a Group I ribozyme. Biochemistry. 38:1999;2982-2990.
14. Doudna J. A., Cate J. H. RNA structure: crystal clear? Curr. Opin. Struct. Biol. 7:1997;310-316.
15. Golden B. L., Gooding A. R., Podell E. R., Cech T. R. A preorganized active site in the crystal structure of the Tetrahymena ribozyme. Science. 282:1998;259-264.
16. Herschlag D., Cech T. R. Catalysis of RNA cleavage by the Tetrahymenathermophila ribozyme. 1. Kinetic description of the reaction of an RNA substrate complementary to the active site. Biochemistry. 29:1990;10159-10171.
17. Herschlag D., Khosla M. Comparison of pH dependencies of the Tetrahymena ribozyme reactions with RNA 2′-substituted and phosphorothioate substrates reveals a rate-limiting conformational step. Biochemistry. 33:1994;5291-5297.
18. Herschlag D., Eckstein F., Cech T. R. Contributions of 2′-hydroxyl groups of the RNA substrate to binding and catalysis by the Tetrahymena ribozyme. An energetic picture of an active site composed of RNA. Biochemistry. 32:1993;8299-8311.
19. Huang G. S., Oas T. G. Submillisecond folding of monomeric lambda repressor. Proc. Natl Acad. Sci. USA. 92:1995;6878-6882.
20. Jackson S. E., Fersht A. R. Folding of chymotrypsin inhibitor 2.1. Evidence for a two-state transition. Biochemistry. 30:1991;10428-10435.
21. Joyce G. F., Inoue T. Structure of the catalytic core of the Tetrahymena ribozyme as indicated by reactive abbreviated forms of the molecule. Nucl. Acids Res. 15:1987;9825-9840.
22. Joyce G. F., van der Horst G., Inoue T. Catalytic activity is retained in the Tetrahymena group I intron despite removal of the large extension of element P5. Nucl. Acids Res. 17:1989;7879-7889.
23. Kiefhaber T. Kinetic traps in lysozyme folding. Proc. Natl Acad. Sci. USA. 92:1995;9029-9033.
24. Lehnert V., Jaeger L., Michel F., Westhof E. New loop-loop tertiary interactions in self-splicing introns of subgroup IC and ID: a complete 3D model of theTetrahymenathermophila ribozyme. Chem. Biol. 3:1996;993-1009.
25. Murphy F. L., Cech T. R. An independently folding domain of RNA tertiary structure within the Tetrahymena ribozyme. Biochemistry. 32:1993;5291-5300.
26. Narlikar G. J., Herschlag D. Mechanistic aspects of enzymatic catalysis: lessons from comparison of RNA and protein enzymes. Annu. Rev. Biochem. 66:1997;19-59.
27. Pan J., Woodson S. A. Folding intermediates of a self-splicing RNA: mispairing of the catalytic core. J. Mol. Biol. 280:1998;597-609.
28. Pan J., Thirumalai D., Woodson S. A. Folding of RNA involves parallel pathways. J. Mol. Biol. 273:1997;7-13.
29. 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.
30. Pan T., Fang X., Sosnick T. Pathway modulation, circular permutation and rapid RNA folding under kinetic control. J. Mol. Biol. 286:1999;721-731.
31. Radford S. E., Dobson C. M., Evans P. A. The folding of hen lysozyme involves partially structured intermediates and multiple pathways. Nature. 358:1992;302-307.
32. Russell R., Herschlag D. Specificity from steric restrictions in the guanosine binding pocket of a group I ribozyme. RNA. 5:1999;158-166.
33. Schindler T., Herrler M., Marahiel M. A., Schmid F. X. Extremely rapid protein folding in the absence of intermediates. Nature Struct. Biol. 2:1995;663-673.
34. Sclavi B., Woodson S., Sullivan M., Chance M. R., Brenowitz M. Time-resolved synchrotron X-ray "footprinting", a new approach to the study of nucleic acid structure and function: application to protein-DNA interactions and RNA folding. J. Mol. Biol. 266:1997;144-159.
35. 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.
36. Strobel S. A., Doudna J. A. RNA seeing double: close-packing of helices in RNA tertiary structure. Trends Biochem. Sci. 22:1997;262-266.
37. Szewczak A. A., Podell E. R., Bevilacqua P. C., Cech T. R. Thermodynamic stability of the P4-P6 domain RNA tertiary structure measured by temperature gradient gel electrophoresis. Biochemistry. 37:1998;11162-11170.
38. Thirumalai D., Woodson S. A. Kinetics of folding of proteins and RNA. Acc. Chem. Res. 29:1996;433-439.
39. 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.
40. Walstrum S. A., Uhlenbeck O. C. The self-splicing RNA of Tetrahymena is trapped in a less active conformation by gel purification. Biochemistry. 29:1990;10573-10576.
41. Zarrinkar P. P., Williamson J. R. Kinetic intermediates in RNA folding. Science. 265:1994;918-924.
42. Zarrinkar P. P., Williamson J. R. The kinetic folding pathway of the Tetrahymena ribozyme reveals possible similarities between RNA and protein folding. Nature Struct. Biol. 3:1996;432-438.
43. Zarrinkar P. P., Wang J., Williamson J. R. Slow folding kinetics of RNase P RNA. RNA. 2:1996;564-573.
44. Zaug A. J., Been M. D., Cech T. R. The Tetrahymena ribozyme acts like an RNA restriction endonuclease. Nature. 324:1986;429-433.
45. Zaug A. J., Grosshans C. A., Cech T. R. Sequence-specific endoribonuclease activity of the Tetrahymena ribozyme: enhanced cleavage of certain oligonucleotide substrates that form mismatched ribozyme-substrate complexes. Biochemistry. 27:1988;8924-8931.