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Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms.


ABSTRACT: RNA molecules with novel functions have revived interest in the accurate prediction of RNA three-dimensional (3D) structure and folding dynamics. However, existing methods are inefficient in automated 3D structure prediction. Here, we report a robust computational approach for rapid folding of RNA molecules. We develop a simplified RNA model for discrete molecular dynamics (DMD) simulations, incorporating base-pairing and base-stacking interactions. We demonstrate correct folding of 150 structurally diverse RNA sequences. The majority of DMD-predicted 3D structures have <4 A deviations from experimental structures. The secondary structures corresponding to the predicted 3D structures consist of 94% native base-pair interactions. Folding thermodynamics and kinetics of tRNA(Phe), pseudoknots, and mRNA fragments in DMD simulations are in agreement with previous experimental findings. Folding of RNA molecules features transient, non-native conformations, suggesting non-hierarchical RNA folding. Our method allows rapid conformational sampling of RNA folding, with computational time increasing linearly with RNA length. We envision this approach as a promising tool for RNA structural and functional analyses.

SUBMITTER: Ding F 

PROVIDER: S-EPMC2390798 | biostudies-literature | 2008 Jun

REPOSITORIES: biostudies-literature

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Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms.

Ding Feng F   Sharma Shantanu S   Chalasani Poornima P   Demidov Vadim V VV   Broude Natalia E NE   Dokholyan Nikolay V NV  

RNA (New York, N.Y.) 20080502 6


RNA molecules with novel functions have revived interest in the accurate prediction of RNA three-dimensional (3D) structure and folding dynamics. However, existing methods are inefficient in automated 3D structure prediction. Here, we report a robust computational approach for rapid folding of RNA molecules. We develop a simplified RNA model for discrete molecular dynamics (DMD) simulations, incorporating base-pairing and base-stacking interactions. We demonstrate correct folding of 150 structur  ...[more]

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