Exploring the dynamics of four RNA-dependent RNA polymerases by a coarse-grained model

In this article, we present a hybrid ENM/MARTINI coarse-grained model and examine the impact of reduced chemical detail on both static and dynamic properties by comparing against explicit atomistic simulations. This methodology complements the advanced molecular characterization and dynamics of proteins for medical and bioengineering applications by developing a fundamental understanding of how the motion and molecular characteristics of proteins, viruses, their precursors, and their interactions with the environment govern their behavior in different populations. As an example, we explore the dynamics of RNA-dependent RNA polymerases (RdRPs) from the following viruses: poliovirus, Coxsackie virus B3, human rhinovirus 16, and foot-and-mouth-disease virus. The hybrid coarse-grained model allows the microsecond time scales of interest for biological functions to be explored. Additionally, the ENM/MARTINI model captures the main features obtained from atomistic MD simulations for each of the RdRPs studied herein, including the higher flexibility of the pinky finger and thumb regions, as well as collective motions that might contribute significantly to the conformational transition between the open and closed states.