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Vlad Cojocaru, Reinhard Klement, Thomas M. Jovin. Loss of G-A base pairs is insufficient for achieving a large opening of U4 snRNA K-turn motif. Nucleic Acids Research, 33, pp. 3435-3446, 2005.

Abstract: Upon binding to the 15.5K protein, two tandem-sheared GA 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 (ke motion) were identified using locally enhanced sampling molecular dynamics simulations, results that agree with experiments. A detailed analysis of the simulations reveals that the ke motion in Kt-U4 is triggered both by loss of GA base pairs in the internal loop and backbone flexibility in the stems. Essential dynamics show that the loss of GA base pairs is correlated along the first mode but anti-correlated along the third mode with the ke motion. Moreover, when enhanced sampling was confined to the internal loop, the RNA adopted an alternative conformation characterized by a sharper kink, opening of GA base pairs and modified stacking interactions. Thus, loss of GA 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 GA base pair formation occurs upon protein binding, thereby stabilizing a selective orientation of the stems.

The cover of Nucleic Acids Research, vol. 33, issue 10 ( features a figure representing this publication

Keywords: RNA K-turn motif, protein-assisted RNA folding, locally enhanced samplic, molecular dynamics simulations, essential dynamics


Posted by Vlad Cojocaru


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