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  The snRNP 15.5K protein folds its cognate K-turn RNA. A combined theoretical and biochemical study

Cojocaru, V., Nottrott, S., Klement, R., & Jovin, T. M. (2005). The snRNP 15.5K protein folds its cognate K-turn RNA. A combined theoretical and biochemical study. RNA, 11(2): 10.1261/rna.7149605, pp. 197-209. Retrieved from http://rnajournal.cshlp.org/content/11/2/197.full.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0012-EA1D-6 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0028-8217-8
Genre: Journal Article

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 Creators:
Cojocaru, V.1, Author              
Nottrott, S.2, Author              
Klement, R.3, Author              
Jovin, T. M.1, Author              
Affiliations:
1Department of Molecular Biology, MPI for biophysical chemistry, Max Planck Society, ou_578628              
2Department of Cellular Biochemistry, MPI for biophysical chemistry, Max Planck Society, ou_578576              
3Emeritus Group Laboratory of Cellular Dynamics, MPI for biophysical chemistry, Max Planck Society, ou_578629              

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Free keywords: Splicing; RNA folding; K-turn motif; molecular dynamics; locally enhanced sampling; induced fit
 Abstract: The human 15.5K protein binds to the 5' stem–loop of U4 snRNA, promotes the assembly of the spliceosomal U4/U6 snRNP, and is required for the recruitment of the 61K protein and the 20/60/90K protein complex to the U4 snRNA. In the crystallographic structure of the 15.5K–U4 snRNA complex, the conformation of the RNA corresponds to the family of kink-turn (K-turn) structural motifs. We simulated the complex and the free RNA, showing how the protein binding and the intrinsic flexibility contribute to the RNA folding process. We found that the RNA is significantly more flexible in the absence of the 15.5K protein. Conformational transitions such as the interconversion between alternative purine stacking schemes, the loss of G-A base pairs, and the opening of the K-turn occur only in the free RNA. Furthermore, the stability of one canonical G-C base pair is influenced both by the binding of the 15.5K protein and the nature of the adjacent structural element in the RNA. We performed chemical RNA modification experiments and observed that the free RNA lacks secondary structure elements, a result in excellent agreement with the simulations. Based on these observations, we propose a protein-assisted RNA folding mechanism in which the RNA intrinsic flexibility functions as a catalyst.

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Language(s): eng - English
 Dates: 2005-01-192005-02
 Publication Status: Published in print
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 Rev. Method: Peer
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Title: RNA
Source Genre: Journal
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Pages: - Volume / Issue: 11 (2) Sequence Number: 10.1261/rna.7149605 Start / End Page: 197 - 209 Identifier: -