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J Struct Biol. 2014 Jan;185(1):48-57. doi: 10.1016/j.jsb.2013.11.007. Epub 2013 Nov 28.

Solution conformation of adenovirus virus associated RNA-I and its interaction with PKR.

Author information

1
Department of Chemistry, University of Manitoba, 144 Dysart Road, Winnipeg, Manitoba R3T 2N2, Canada.
2
Department of Chemistry, University of Manitoba, 144 Dysart Road, Winnipeg, Manitoba R3T 2N2, Canada; School of Biosciences, University of Birmingham, Birmingham B152TT, UK.
3
Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. Ks. Trojdena 4, Warsaw 02-109, Poland.
4
Department of Chemistry, University of Manitoba, 144 Dysart Road, Winnipeg, Manitoba R3T 2N2, Canada; Manitoba Institute for Materials, University of Manitoba, 144 Dysart Road, Winnipeg, Manitoba R3T 2N2, Canada.
5
NCMH Laboratory, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, UK.
6
Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. Ks. Trojdena 4, Warsaw 02-109, Poland; Laboratory of Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, Poznan 61-614, Poland.
7
Department of Chemistry, University of Manitoba, 144 Dysart Road, Winnipeg, Manitoba R3T 2N2, Canada; Department of Biochemistry and Medical Genetics, University of Manitoba, 144 Dysart Road, Winnipeg, Manitoba R3T 2N2, Canada. Electronic address: Sean.McKenna@umanitoba.ca.

Abstract

Adenovirus virus-associated RNA (VAI) provides protection against the host antiviral response in part by inhibiting the interferon-induced double stranded RNA-activated protein kinase (PKR). VAI consists of three base-paired regions; the apical stem responsible for the interaction with double-stranded RNA binding motifs (dsRBMs) of PKR, the central stem required for inhibition, and the terminal stem. The solution conformation of VAI and VAI lacking the terminal stem were determined using SAXS that suggested extended conformations that are in agreement with their secondary structures. Solution conformations of VAI lacking the terminal stem in complex with the dsRBMs of PKR indicated that the apical stem interacts with both dsRNA-binding motifs whereas the central stem does not. Hydrodynamic properties calculated from ab initio models were compared to experimentally determined parameters for model validation. Furthermore, SAXS envelopes were used as a constraint for the in silico modeling of tertiary structure for RNA and RNA-protein complex. Finally, full-length PKR was also studied, but concentration-dependent changes in hydrodynamic parameters prevented ab initio shape determination. Taken together, results provide an improved structural framework that further our understanding of the role VAI plays in evading host innate immune responses.

KEYWORDS:

AS; AUC; Adenovirus; CS; D(max); DLS; EM; NSD; PKR; Protein–RNA interactions; RNA-activated protein kinase; SAXS; SEC; Small angle X-ray scattering; TS; VA(I); VA(I) RNA; VA(I) lacking the terminal stem; VA(I)AS; VA(IΔ)TS; adenovirus virus-associated RNA; analytical ultracentrifugation; apical stem-loop; apical stem-loop of VA(I); central stem-loop; double-stranded RNA binding domains; dsRBMs; dsRNA; dynamic light scattering; eIF2; electron microscopy; electron pair-distance distribution function; eukaryotic initiation factor 2; hydrodynamic radius; in silico structure determination; maximum particle dimension; normalized spatial discrepancy; p(r) function; r(G); r(H); radius of gyration; s(20)(w); sedimentation co-efficient of water at 20°C; size exclusion chromatography; small angle X-ray scattering; terminal stem-loop

PMID:
24291322
DOI:
10.1016/j.jsb.2013.11.007
[Indexed for MEDLINE]

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