Coarse Graining RNA Nanostructures for Molecular Dynamics Simulations

TL;DR

This paper introduces coarse-grained models for RNA nanostructures that significantly extend simulation timescales, enabling the study of large RNA systems with reduced computational cost while maintaining structural accuracy.

Contribution

The study develops and compares multi-bead coarse-grained RNA models that balance simplicity and accuracy, allowing microsecond-scale simulations of large RNA molecules.

Findings

3-beads-per-nucleotide models are effective across different RNA conformations

Models with universal parameters perform comparably to detailed backbone models

Simulations reach microsecond timescales, three orders longer than atomistic models

Abstract

A series of coarse-grained models have been developed for the study of the molecular dynamics of RNA nanostructures. The models in the series have one to three beads per nucleotide and include different amounts of detailed structural information. Such a treatment allows us to reach, for the systems of thousands of nucleotides, a time scale of microseconds (i.e. by three orders of magnitude longer than in the full atomistic modelling) and thus to enable simulations of large RNA polymers in the context of bionanotechnology. We find that the 3-beads-per-nucleotide models, described by a set of just a few universal parameters, are able to describe different RNA conformations and are comparable in structural precision to the models where detailed values of the backbone P-C4' dihedrals taken from a reference structure are included. These findings are discussed in the context of the RNA conformation classes.