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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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Cojocaru, V.1, Autor           
Klement, R.2, Autor           
Jovin, T. M.1, Autor           
Affiliations:
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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Schlagwörter: K-turn motif; G-A base pairs; molecular dynamics simulations; locally enhanced sampling; principal component analysis; molecular dynamics
 Zusammenfassung: 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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Sprache(n): eng - English
 Datum: 2005-06-172005-06
 Publikationsstatus: Erschienen
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 Identifikatoren: eDoc: 226712
URI: http://nar.oxfordjournals.org/cgi/content/full/33/10/3435
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Titel: Nucleic Acids Research
Genre der Quelle: Zeitschrift
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Ort, Verlag, Ausgabe: -
Seiten: - Band / Heft: 33 (10) Artikelnummer: doi:10.1093/nar/gki664 Start- / Endseite: 3435 - 3446 Identifikator: -