Exploration micromechanism of VP35 IID interaction and recognition dsRNA: A molecular dynamics simulation

Abstract

Multifunctional viral protein (VP35) encoded by the highly pathogenic Ebola viruses (EBOVs) can antagonize host double-stranded RNA (dsRNA) sensors and immune response because of the simultaneous recognition of dsRNA backbone and blunt ends. Mutation of select hydrophobic conserved basic residues within the VP35 inhibitory domain (IID) abrogates its dsRNA-binding activity, and impairs VP35-mediated interferon (IFN) antagonism. Herein the detailed binding mechanism between dsRNA and WT, single mutant, and double mutant were investigated by all-atom molecular dynamics (MD) simulation and binding energy calculation. R312A/R322A double mutations results in a completely different binding site and orientation upon the structure analyses. The calculated binding free energy results reveal that R312A, R322A, and K339A single mutations decrease the binding free energies by 17.82, 13.18, and 13.68 kcal mol , respectively. The binding energy decomposition indicates that the strong binding affinity of the key residues is mainly due to the contributions of electrostatic interactions in the gas phase, where come from the positively charged side chain and the negatively charged dsRNA backbone. R312A, R322A, and K339A single mutations have no significant effect on VP35 IID conformation, but the mutations influence the contributions of electrostatic interactions in the gas phase. The calculated results reveal that end-cap residues which mainly contribute VDW interactions can recognize and capture dsRNA blunt ends, and the central basic residues (R312, R322, and K339) which mainly contribute favorable electrostatic interactions with dsRNA backbone can fix dsRNA binding site and orientation. Proteins 2017; 85:1008-1023. © 2017 Wiley Periodicals, Inc.

Human transbodies that interfere with the functions of Ebola virus VP35 protein in genome replication and transcription and innate immune antagonism

“…Therefore, it is plausible that host innate immunity rescued by R9-HuscFv3 occurred via obstruction or suppression of these critical IID residues. R9-HuscFv8 showed comparable effectiveness to R9-HuscFv3 relative to host innate immunity restoration, which could be due to binding of the transbody to R322 and K339 of the central basic patch, which is important for the interaction and recognition of dsRNA 53 . In addition, R9-HuscFv8 was predicted to bind to I340 of the end cap and to S272, C275, I278, and Q279, which should disrupt dsRNA binding.…”

“…Plasmids for expressing Zaire EBOV NP, VP35, VP30, and L were designed as previously described 53 with modifications. Optimized DNA coding for EBOV NP (accession MF801600), NP-IRES-VP35 (accession MF801600), VP30 (accession MF801601), and L (accession MF801602) was synthesized and cloned into the pCI-neo mammalian expression vector (with CMV promoter) (GenScript).…”

Exploring the Binding Mechanism and Dynamics of EndoMS/NucS to Mismatched dsDNA

“…All the MD simulations included two stages: Minimization and equilibration [45,46,47]. The minimization included three steps: The systems were first subjected to 2500 steps of steep descent movements, followed by 2500 steps of conjugate gradient minimization to remove the bad clashes between solute and solvent.…”