Probing the folding landscape of the Tetrahymena ribozyme: Commitment to form the native conformation is late in the folding pathway

Journal of Molecular Biology

Volumn 308, Issue 5, 2001, Pages 839-851

  Russell, Rick ^a   Herschlag, Daniel ^a  

^a STANFORD UNIVERSITY   (United States)

Author keywords

Folding landscape; Group I intron; Misfolding; Ribozyme; RNA folding

Indexed keywords

RIBOZYME; RNA;

ARTICLE; ENZYME CONFORMATION; INTRON; MODEL; NONHUMAN; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; RNA ANALYSIS; STRUCTURE ANALYSIS; TEMPERATURE SENSITIVITY; TETRAHYMENA;

TETRAHYMENA;

EID: 0035906731     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.2001.4751     Document Type: Article

References (39)

1. Kinetic intermediates in RNA folding
2. Fingerprinting the folding of a group I precursor RNA
3. Kinetic pathway for folding of the Tetrahymena ribozyme revealed by three UV-inducible crosslinks
4. The kinetic folding pathway of the Tetrahymena ribozyme reveals possible similarities between RNA and protein folding
5. Folding of RNA involves parallel pathways
6. Folding intermediates of a self-splicing RNA: Mispairing of the catalytic core
7. RNA folding at millisecond intervals by synchrotron hydroxyl radical footprinting
8. Kinetic intermediates trapped by native interactions in RNA folding
9. Fast folding mutants of the Tetrahymena group I ribozyme reveal a rugged folding energy landscape
10. An optimal Mg(2+) concentration for kinetic folding of the Tetrahymena ribozyme
11. New pathways in folding of the Tetrahymena group I RNA enzyme
12. The effect of long-range loop-loop interactions on folding of the Tetrahymena self-splicing RNA
13. Magnesium-dependent folding of self-splicing RNA: Exploring the link between cooperativity, thermodynamics, and kinetics
14. Fast folding of a ribozyme by stabilizing core interactions: Evidence for multiple folding pathways in RNA
15. Small angle X-ray scattering reveals a compact intermediate in RNA folding
16. Hierarchy and dynamics of RNA folding
17. Exposing the kinetic traps in RNA folding
18. Kinetics of folding of proteins and RNA
19. Thermodynamics and kinetics of base-pairing and of DNA and RNA self-assembly and helix coil transition
20. RNA folding causes secondary structure rearrangement
21. Quantifying the energetic interplay of RNA tertiary and secondary structure interactions
22. Catalysis of RNA cleavage by the Tetrahymena thermophila ribozyme. 1. Kinetic description of the reaction of an RNA substrate complementary to the active site
23. Electrophoretic separation of complexes involved in the splicing of precursors to mRNAs
24. Analysis of rate-determining conformational changes during self-splicing of the Tetrahymena intron
25. A single molecule study of RNA catalysis and folding
26. Stability and cooperativity of individual tertiary contacts in RNA revealed through chemical denaturation
27. Folding mechanism of the Tetrahymena ribozyme P4-P6 domain
28. Multiple folding pathways for the P4-P6 RNA domain
29. 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
30. An independently folding domain of RNA tertiary structure within the Tetrahymena ribozyme
31. Predicting thermodynamic properties of RNA
32. Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base-pairs
33. Representation of the secondary and tertiary structure of group I introns
34. New loop-loop tertiary interactions in self-splicing introns of subgroup IC and ID: A complete 3D model of the Tetrahymena thermophila ribozyme
35. 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
36. Alternative secondary structures in the 5′ exon affect both forward and reverse self-splicing of the Tetrahymena intervening sequence RNA
37. Dynamics of ribozyme binding of substrate revealed by fluorescence-detected stopped-flow methods
38. Evidence for processivity and two-step binding of the RNA substrate from studies of J1/2 mutants of the Tetrahymena ribozyme