Coarse-grained RNA model for the Martini 3 force field.

Area of Science:

• Computational Biology
• Biophysics
• Molecular Modeling

Background:

• Coarse-grained models are essential for simulating large biomolecular systems.
• Existing RNA models face limitations in accuracy and stability for complex systems.

Purpose of the Study:

• To develop a coarse-grained RNA model compatible with the Martini 3 force field.
• To enhance the simulation capabilities for large RNA-containing complexes.

Main Methods:

• Parameterization using top-down and bottom-up approaches, including solvent partitioning and potential of mean force calculations.
• Refinement of bonded interactions using atomistic simulations of double-stranded RNA.
• Incorporation of an elastic network for structural integrity.

Main Results:

• The Martini 3 RNA model accurately captures properties of bases, single- and double-stranded RNA, and RNA-protein complexes.
• Improved numerical stability allows simulations of large complexes like ribosomes with a 20 fs time step.
• Enhanced agreement with all-atom models and experimental data.

Conclusions:

• The developed Martini 3 RNA model facilitates realistic, large-scale explicit-solvent molecular dynamics simulations.
• This model represents a significant advancement for studying complex RNA systems.
• It enables more accurate and efficient investigation of RNA's role in biological processes.