Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery: Bridging Experiments and Computations - September 10-14, 2014, Istanbul, Turkey

Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery Poster Session II

77-POS Board 30 Modeling RNA Dynamics Using Elastic Network Models Giovanni Pinamonti , Sandro Bottaro, Cristian Micheletti, Giovanni Bussi. SISSA - International School for Advaced Studies, Trieste, Italy. The number of known fundamental functions of RNA

in the cell has been steadily increasing in the last decades. The function of RNA molecules is often, though not always, intimately connected to their dynamics. For this reason, several experimental and computational efforts are being spent to characterize the internal dynamics of RNA. The scope of atomistic molecular dynamics (MD) simulations, which is presently limited due to its computational cost, can be aptly complemented by suitable coarse-grained models. These include elastic network models (ENM) where a biomolecule is represented as a set of

harmonic oscillators. For proteins, ENM's predictions have been shown to successfully reproduce the principal components of motion derived from all-atoms MD simulations. As of today, a few works have studied the possibility to extend this modelling strategy to nucleic acid dynamics. We here considered four widely different RNA systems, testing the predictions of various ENMs, differing for the level of coarse-graining, against results obtained from the analysis of extensive MD trajectories. We report on the different performance of the considered ENMs and discuss their effectiveness in capturing RNA dynamics against MD references.

130