Molecular Dynamics Simulations of Protein RNA Complexes by Using an Advanced Electrostatic Model.

ABSTRACT: Protein-RNA interactions are integral to the biological functions of RNA. It is well recognized that molecular dynamics (MD) simulations of protein-RNA complexes are more challenging than those of each component. The difficulty arises from the strong electrostatic interactions and the delicate balance between various types of physical forces at the interface. Previously, MD simulations of protein-RNA complexes have predominantly employed fixed-charge force fields. Although force field modifications have been developed to address problems identified in the simulations, some protein-RNA structures are still hard to reproduce by simulations. Here, we present MD simulations of two representative protein-RNA complexes using the AMOEBA polarizable force field. The van der Waals parameters were r

SUBMITTER: Jing Z 

PROVIDER: S-EPMC9530969 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature