RNA-protein complexes and force field polarizability

Molecular dynamic (MD) simulations offer a way to study biomolecular interactions and their dynamics at the atomistic level which is not possible with the current experimental methods. There are only a few studies of RNA-protein complexes in MD simulations, and here we wanted to study how force fields differ when simulating RNA-protein complexes. We tested three non-polarizable force fields: Amber protein force fields ff14SB and ff19SB with RNA force field OL3, and the all-atom OPLS4 force field. Due to the highly charged and polar nature of RNA, we also tested the polarizable AMOEBA force field. Our results show that the non-polarizable force fields overestimate the electrostatic interactions between the RNA and the protein which leads to compact and stable complexes. This effect is not seen in the polarizable force field, but it is computationally much more demanding. As a conclusion, all the tested force fields can be used to simulate RNA-protein complexes. If computational resources are not limited or if lengthy simulations are not needed for the studied problem, the polarizable force field AMOEBA is the best choice.