title: 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-1, 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.
authors.affiliation: National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei 230029, People's Republic of China.
authors.forename: Yan-Jun
authors.identifier: 0000-0003-3360-5156
authors.initials: YJ
authors.lastname: Zhang
authors.affiliation: National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei 230029, People's Republic of China.
authors.forename: Jing-Na
authors.initials: JN
authors.lastname: Ding
authors.affiliation: National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei 230029, People's Republic of China.
authors.forename: Hui
authors.initials: H
authors.lastname: Zhong
authors.affiliation: National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei 230029, People's Republic of China.
authors.forename: Ju-Guang
authors.initials: JG
authors.lastname: Han
mesh_terms: D000409:Alanine / Q000737:chemistry* / Q000378:metabolism; D019943:Amino Acid Substitution; D001120:Arginine / Q000737:chemistry* / Q000378:metabolism; D001665:Binding Sites; D029043:Ebolavirus / Q000737:chemistry*; D054884:Host-Pathogen Interactions; D056004:Molecular Dynamics Simulation; D009154:Mutation; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D000072756:Protein Conformation, alpha-Helical; D000072757:Protein Conformation, beta-Strand; D054730:Protein Interaction Domains and Motifs; D012330:RNA, Double-Stranded / Q000737:chemistry* / Q000378:metabolism; D055672:Static Electricity; D013816:Thermodynamics; D054334:Viral Regulatory and Accessory Proteins / Q000737:chemistry* / Q000378:metabolism
chemical_list: D012330:RNA, Double-Stranded; C080980:VP35 protein, filovirus; D054334:Viral Regulatory and Accessory Proteins; D001120:Arginine; D000409:Alanine
keywords: Ebola virus; MD simulation; activation of host RIG-I-like receptors; dsRNA recognition; interaction mechanism; mutation