ArticleRNA (New York, N.Y.)2013
Recognition of viral RNA stem-loops by the tandem double-stranded RNA binding domains of PKR.
Article in RNA (New York, N.Y.), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 31 citations in OpenAlex.
- Genetic alteration of SJ293TS cells and modification of serum-free media enhances lentiviral vector production.Molecular therapy. Methods & clinical development · 2024Article
- Small Extracellular Vesicle Enrichment of a Retrotransposon-Derived Double-Stranded RNA: A Means to Avoid Autoinflammation?Biomedicines · 2021Article
- Human DDX17 Unwinds Rift Valley Fever Virus Non-Coding RNAs.International journal of molecular sciences · 2020Article
- Analytical ultracentrifuge: an ideal tool for characterization of non-coding RNAs.European biophysics journal : EBJ · 2020Review
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- Nanoscale Structure Determination of Murray Valley Encephalitis and Powassan Virus Non-Coding RNAs.Viruses · 2020Article
- Solution Structure of C. elegans UNC-6: A Nematode Paralogue of the Axon Guidance Protein Netrin-1.Biophysical journal · 2019Article
- Exosomes derived from HIV-1-infected cells promote growth and progression of cancer via HIV TAR RNA.Nature communications · 2018Article
- Nanoscale Assembly of High-Mobility Group AT-Hook 2 Protein with DNA Replication Fork.Biophysical journal · 2017Article
- Human noncoding RNA 886 (nc886) adopts two structurally distinct conformers that are functionally opposing regulators of PKR.RNA (New York, N.Y.) · 2017Article
- Analysis of RNA structure using small-angle X-ray scattering.Methods (San Diego, Calif.) · 2017Article
- Impact of the structural integrity of the three-way junction of adenovirus VAI RNA on PKR inhibition.PloS one · 2017Article
- Dynamic light scattering: a practical guide and applications in biomedical sciences.Biophysical reviews · 2016Review
- Article
- The β-lactamase gene regulator AmpR is a tetramer that recognizes and binds the D-Ala-D-Ala motif of its repressor UDP-N-acetylmuramic acid (MurNAc)-pentapeptide.The Journal of biological chemistry · 2015Article
- Biophysical Characterization of G-Quadruplex Recognition in the PITX1 mRNA by the Specificity Domain of the Helicase RHAU.PloS one · 2015Article
- Conformational itinerary of Pseudomonas aeruginosa 1,6-anhydro-N-acetylmuramic acid kinase during its catalytic cycle.The Journal of biological chemistry · 2014Article
- Activation of 2' 5'-oligoadenylate synthetase by stem loops at the 5'-end of the West Nile virus genome.PloS one · 2014Article
- Binding of G-quadruplexes to the N-terminal recognition domain of the RNA helicase associated with AU-rich element (RHAU).The Journal of biological chemistry · 2013Article
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In humans, the double-stranded RNA (dsRNA)-activated protein kinase (PKR) is expressed in late stages of the innate immune response to viral infection by the interferon pathway. PKR consists of tandem dsRNA binding motifs (dsRBMs) connected via a flexible linker to a Ser/Thr kinase domain. Upon interaction with viral dsRNA, PKR is converted into a catalytically active enzyme capable of phosphorylating a number of target proteins that often results in host cell translational repression. A number of high-resolution structural studies involving individual dsRBMs from proteins other than PKR have highlighted the key features required for interaction with perfectly duplexed RNA substrates. However, viral dsRNA molecules are highly structured and often contain deviations from perfect A-form RNA helices. By use of small-angle X-ray scattering (SAXS), we present solution conformations of the tandem dsRBMs of PKR in complex with two imperfectly base-paired viral dsRNA stem-loops; HIV-1 TAR and adenovirus VA(I)-AS. Both individual components and complexes were purified by size exclusion chromatography and characterized by dynamic light scattering at multiple concentrations to ensure monodispersity. SAXS ab initio solution conformations of the individual components and RNA-protein complexes were determined and highlight the potential of PKR to interact with both stem and loop regions of the RNA. Excellent agreement between experimental and model-based hydrodynamic parameter determination heightens our confidence in the obtained models. Taken together, these data support and provide a framework for the existing biochemical data regarding the tolerance of imperfectly base-paired viral dsRNA by PKR.
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