Simulating Dynamics in RNA–Protein Complexes

Simulation of RNA–protein complexes presents new challenges for computational studies. While the fields of protein folding and docking of protein complexes have matured sufficiently so that experimental and computational methods complement and cross-validate each other, methods for RNA folding and docking of RNA to proteins are still in their infancy. Part of the difficulty lies in the complex interactions of RNA with ions and water that differ considerably from those of proteins, due to the extreme electronegativity of RNA, and result in unique dynamics. Here we address challenging issues in the simulation of RNA and its interactions with solvent, ions, and proteins. A general discussion of the preparation and simulation of large RNA–protein systems with divalent cations and modified bases is given, followed by a critical summary of methods for analyzing the resulting MD trajectories.