Polarizable force field for RNA based on the classical drude oscillator

Area of Science:

• Computational Chemistry
• Molecular Dynamics
• Structural Biology

Background:

• RNA molecules exhibit complex dynamics and folding influenced by base pairing, hydration, stacking, and ion interactions.
• Accurately modeling RNA structure in molecular dynamics simulations requires accounting for electronic polarization.
• Existing empirical force fields face challenges in representing these intricate RNA features.

Purpose of the Study:

• To develop and validate a polarizable force field for RNA using the classical Drude oscillator model.
• To improve the accuracy of molecular dynamics simulations for RNA structures and dynamics.

Main Methods:

• Developed a polarizable force field for RNA by extending the Drude-2017 nucleic acid force field.
• Utilized the classical Drude oscillator model, representing electronic degrees of freedom with charged particles.
• Parametrized the force field against quantum mechanical data for base stacking and conformational energies.
• Validated the force field using molecular dynamics simulations of various RNA sequences, including duplexes, stem-loops, and tertiary structures with Mg2+ ions.

Main Results:

• The Drude-2017 RNA force field successfully reproduces key properties of RNA structures.
• Accurate conformational sampling of the 2'-hydroxyl group was achieved.
• Crucial interactions between RNA and Mg2+ ions were effectively modeled.

Conclusions:

• The developed polarizable force field enhances the accuracy of molecular dynamics simulations for RNA.
• This advancement enables more reliable studies of RNA folding, dynamics, and interactions with ions.
• The Drude-2017 RNA force field provides a valuable tool for investigating complex RNA systems.