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  Loss of G-A base pairs is insufficient for achieving a large opening of U4 snRNA K-turn motif

Cojocaru, V., Klement, R., & Jovin, T. M. (2005). Loss of G-A base pairs is insufficient for achieving a large opening of U4 snRNA K-turn motif. Nucleic Acids Research, 33(10): doi:10.1093/nar/gki664, pp. 3435-3446. Retrieved from http://nar.oxfordjournals.org/cgi/content/full/33/10/3435.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0012-E8F3-0 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0027-D9A7-7
Genre: Journal Article

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Cojocaru, V.1, Author              
Klement, R.2, Author              
Jovin, T. M.1, Author              
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1Department of Molecular Biology, MPI for biophysical chemistry, Max Planck Society, ou_578628              
2Emeritus Group Laboratory of Cellular Dynamics, MPI for biophysical chemistry, Max Planck Society, ou_578629              

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Free keywords: K-turn motif; G-A base pairs; molecular dynamics simulations; locally enhanced sampling; principal component analysis; molecular dynamics
 Abstract: Upon binding to the 15.5K protein, two tandem-sheared G-A base pairs are formed in the internal loop of the kink turn motif of U4 snRNA (Kt-U4). We have reported that the folding of Kt-U4 is assisted by protein binding. Unstable interactions that contribute to a large opening of the free RNA (“k-e motion”) were identified using locally enhanced sampling molecular dynamics (LES-MD) simulations, results that agree with experiment. A detailed analysis of the simulations reveals that the k-e motion in Kt-U4 is triggered both by loss of G-A base pairs in the internal loop and backbone flexibility in the stems. Essential dynamics show that the loss of G-A base pairs is correlated along the first mode but anti-correlated along the third mode with the k-e motion. Moreover, when enhanced sampling was confined to the internal loop, the RNA adopted an alternative conformation characterized by a sharper kink, opening of G-A base pairs and, modified stacking interactions. Thus, loss of G-A base pairs is insufficient for achieving a large opening of the free RNA. These findings, supported by previously published RNA structure probing experiments, suggest that G-A base pair formation occurs upon protein binding, thereby stabilizing a selective orientation of the stems.

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Language(s): eng - English
 Dates: 2005-06-172005-06
 Publication Status: Published in print
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Title: Nucleic Acids Research
Source Genre: Journal
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Pages: - Volume / Issue: 33 (10) Sequence Number: doi:10.1093/nar/gki664 Start / End Page: 3435 - 3446 Identifier: -