Single-molecule studies of group II intron ribozymes

Group II intron ribozymes fold into their native structure by a unique stepwise process that involves an initial slow compaction followed by fast formation of the native state in a Mg²⁺-dependent manner. Single-molecule fluorescence reveals three distinct on-pathway conformations in dynamic equilibr...

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Published inProceedings of the National Academy of Sciences - PNAS Vol. 105; no. 37; pp. 13853 - 13858
Main Authors Steiner, Miriam, Karunatilaka, Krishanthi S, Sigel, Roland K.O, Rueda, David
Format Journal Article
LanguageEnglish
Published United States National Academy of Sciences 16.09.2008
National Acad Sciences
Subjects
Binding sites
Biological Sciences
Catalysis
Dynamic structural analysis
Enzyme Activation
Fluorescence
Fluorescence Resonance Energy Transfer
Histograms
Introns
Introns - genetics
Kinetics
Magnesium
Magnesium - chemistry
Magnesium - metabolism
Models, Molecular
Molecules
Protein Folding
Protein Structure, Tertiary
Ribozymes
RNA
RNA, Ribosomal, Self-Splicing - chemistry
RNA, Ribosomal, Self-Splicing - classification
RNA, Ribosomal, Self-Splicing - genetics
RNA, Ribosomal, Self-Splicing - metabolism
Saccharomyces cerevisiae - enzymology
Saccharomyces cerevisiae - genetics
Splicing
Substrate Specificity
Time Factors
Trajectories
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Summary:Group II intron ribozymes fold into their native structure by a unique stepwise process that involves an initial slow compaction followed by fast formation of the native state in a Mg²⁺-dependent manner. Single-molecule fluorescence reveals three distinct on-pathway conformations in dynamic equilibrium connected by relatively small activation barriers. From a most stable near-native state, the unobserved catalytically active conformer is reached. This most compact conformer occurs only transiently above 20 mM Mg²⁺ and is stabilized by substrate binding, which together explain the slow cleavage of the ribozyme. Structural dynamics increase with increasing Mg²⁺ concentrations, enabling the enzyme to reach its active state.
Bibliography:ObjectType-Article-1
SourceType-Scholarly Journals-1
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Author contributions: R.K.O.S. and D.R. designed research; M.S. and K.S.K. performed research; M.S., R.K.O.S., and D.R. analyzed data; and M.S., R.K.O.S., and D.R. wrote the paper.
Edited by Ignacio Tinoco, Jr., University of California, Berkeley, CA, and approved July 28, 2008
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.0804034105