Steered molecular dynamics identifies critical residues of the Nodamura virus B2 suppressor of RNAi.

ABSTRACT: Nearly all RNA viruses produce double-stranded RNA (dsRNA) during their replication cycles--an important pathogen-associated molecular pattern recognized by the RNA interference (RNAi) pathway in invertebrates and plants. Nodamura virus (NoV) encodes a suppressor of RNA silencing termed B2, which binds to dsRNA and prevents the initiation of RNAi as well as the loading of silencing complexes. Using the published crystal structure of NoV-B2, we performed a series of molecular dynamics (MD) simulations to determine the relative electrostatic and van der Waals contributions of various residues in binding dsRNA, identifying four novel potential interactors: R56, E48, P68 and R69. Additionally, steered MD was used to simulate the binding affinity of NoV-B2 sequences bearing substitutions at pos

SUBMITTER: Allen WJ 

PROVIDER: S-EPMC5862041 | biostudies-literature | 2014 Mar

REPOSITORIES: biostudies-literature