Fast folding of a ribozyme by stabilizing core interactions: Evidence for multiple folding pathways in RNA

Journal of Molecular Biology

Volumn 296, Issue 1, 2000, Pages 133-144

  Pan, Jie ^a   Deras, Michael L ^b   Woodson, Sarah A ^a  

^a University of Maryland   (United States)

^b JOHNS HOPKINS UNIVERSITY   (United States)

Author keywords

Group I intron; Hydroxyl radical cleavage; RNA folding; X ray footprinting

Indexed keywords

RIBOZYME; RNA;

ARTICLE; CONFORMATIONAL TRANSITION; ENZYME ACTIVE SITE; ENZYME ACTIVITY; INTRON; NONHUMAN; POINT MUTATION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE; PROTEIN STABILITY; RNA ANALYSIS; TETRAHYMENA;

PROTOZOA; TETRAHYMENA;

EID: 0034635353     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.3439     Document Type: Article

References (46)

1. The time dependence of chemical modification reveals slow steps in the folding of a group I ribozyme
2. Thermal unfolding of a group I ribozyme: The low-temperature transition is primarily disruption of tertiary structure
3. Intermediates and barrier crossing in a random energy-model (with applications to protein folding)
4. Crystal structure of a group I ribozyme domain: Principles of RNA packing
5. Representation of the secondary and tertiary structure of group I introns
6. Iron(II)-ethylene-diaminetetraacetic acid catalyzed cleavage of RNA and DNA oligonucleotides: Similar reactivity toward single- and double-stranded forms
7. Visualizing the higher order folding of a catalytic, RNA molecule
8. Protein folding in the landscape perspective: Chevron plots and non-Arrhenius kinetics
9. Assembly of an exceptionally stable RNA tertiary interface in a group I ribozyme
10. Self-assembly of a group I intron active site from its component tertiary structural domains
11. Kinetic pathway for folding of the Tetrahymena ribozyme revealed by three UV-inducible crosslinks
12. Parallel worlds
13. Self-splicing of the Tetrahymena pre-rRNA is decreased by misfolding during transcription
14. Fingerprinting the folding of a group I precursor RNA
15. Tertiary structure in transfer ribonucleic acids
16. A preorganized active site in the crystal structure of the Tetrahymena ribozyme
17. In vitro genetic analysis of the hinge region between helical elements P5-P4-P6 and P7-P3-P8 in the sunY group I self-splicing intron
18. Long-range interaction between the P2.1 and P9.1 peripheral domains of the Tetrahymena ribozyme
19. 2+, and in the presence of substrate
20. Monitoring of the cooperative unfolding of the sunY group I intron of bacteriophage T4. The active form of the sunY ribozyme is stabilized by multiple interactions with 3' terminal intron components
21. Catalytic activity is retained in the Tetrahymena group I intron despite removal of the large extension of element P5
22. Two major tertiary folding transitions of the Tetrahymena catalytic RNA
23. Defining the inside and outside of a catalytic RNA molecule
24. New loop-loop tertiary interactions in self-splicing introns of subgroup IC and ID: A complete 3D model of the Tetrahymena thermophila ribozyme
25. An independently folding domain of RNA tertiary structure within the Tetrahymena ribozyme
26. GAAA tetraloop and conserved bulge stabilize tertiary structure of a group I intron domain
27. Facilitation of group I splicing in vivo: Misfolding of the Tetrahymena IVS and the role of ribosomal RNA exons
28. Protein and Mg(2+)-induced conformational changes in the S15 binding site of 16 S ribosomal RNA
29. Intermediates and kinetic traps in the folding of a large ribozyme revealed by circular dichroism and UV absorbance spectroscopies and catalytic activity
30. Folding intermediates of a self-splicing RNA: Mispairing of the catalytic core
31. The effect of long-range loop-loop interactions on folding of the Tetrahymena self-splicing RNA
32. Folding of RNA involves parallel pathways
33. Magnesium-dependent folding of self-splicing RNA: Exploring the link between cooperativity, thermodynamics, and kinetics
34. Pathway modulation, circular permutation and rapid RNA folding under kinetic control
35. Fast folding mutants of the Tetrahymena group I ribozyme reveal a rugged folding energy landscape
36. New pathways in folding of the Tetrahymena group I RNA enzyme
37. RNA folding at millisecond intervals by synchrotron hydroxyl radical footprinting
38. Following the folding of RNA with time-resolved synchrotron X-ray foot-printing
39. From the minimal models to real proteins: Time scales for protein folding kinetics
40. Kinetics of folding of protein and RNA
41. Exposing the kinetic traps in RNA folding
42. Kinetic intermediates trapped by native interactions in RNA folding
43. Kinetic intermediates in RNA folding
44. The kinetic folding pathway of the Tetrahymena ribozyme reveals possible similarities between RNA and protein folding
45. Sequence-specific endoribonuclease of the Tetrahymena ribozyme: Enhanced cleavage of certain oligonucleotide substrates that form mismatched ribozyme-substrate complexes