Structural analysis of adenovirus VAI RNA defines the mechanism of inhibition of PKR

Biophys J. 2015 Feb 3;108(3):748-57. doi: 10.1016/j.bpj.2014.12.014.

Abstract

Protein kinase R (PKR) is activated by dsRNA produced during virus replication and plays a major role in the innate immunity response to virus infection. In response, viruses have evolved multiple strategies to evade PKR. Adenovirus virus-associated RNA-I (VAI) is a short, noncoding transcript that functions as an RNA decoy to sequester PKR in an inactive state. VAI consists of an apical stem-loop, a highly structured central domain, and a terminal stem. Chemical probing and mutagenesis demonstrate that the central domain is stabilized by a pseudoknot. A structural model of VAI was obtained from constraints derived from chemical probing and small angle x-ray scattering (SAXS) measurements. VAI adopts a flat, extended conformation with the apical and terminal stems emanating from a protuberance in the center. This model reveals how the apical stem and central domain assemble to produce an extended duplex that is precisely tuned to bind a single PKR monomer with high affinity, thereby inhibiting activation of PKR by viral dsRNA.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Base Sequence
  • Models, Molecular
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Protein Binding
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • RNA, Viral / chemistry*
  • RNA, Viral / genetics
  • Scattering, Small Angle
  • X-Ray Diffraction
  • eIF-2 Kinase / antagonists & inhibitors*
  • eIF-2 Kinase / chemistry
  • eIF-2 Kinase / metabolism

Substances

  • RNA, Viral
  • adenovirus associated RNA
  • eIF-2 Kinase