G. Pinamonti, S. Bottaro, C. Micheletti and G. Bussi
Elastic network models for RNA: a comparative assessment with molecular dynamics and SHAPE experiments
Nucl. Acids Res., 2015,43 , 7260
Link to online article
Abstract
Elastic network models (ENMs) are valuable and
efficient tools for characterizing the collective
internal dynamics of proteins based on the
knowledge of their native structures. The increasing
evidence that the biological functionality of RNAs
is often linked to their innate internal motions,
poses the question of whether ENM approaches
can be successfully extended to this class of
biomolecules. This issue is tackled here by
considering various families of elastic networks
of increasing complexity applied to a representative
set of RNAs. The fluctuations predicted by the
alternative ENMs are stringently validated by
comparison against extensive molecular dynamics
simulations and SHAPE experiments. We find
that simulations and experimental data are
systematically best reproduced by either an all-atom
or a three-beads-per-nucleotide representation
(sugar-base-phosphate), with the latter arguably
providing the best balance of accuracy and
computational complexity.