130
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.
