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Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering
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Analysis of PKR structure by small-angle scattering.

Jennifer VanOudenhove1, Eric Anderson, Susan Krueger

  • 1Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA.

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Protein kinase R (PKR), vital for antiviral defense, has flexible regions allowing it to adapt. These intrinsically unstructured regions enable PKR to dimerize effectively when interacting with RNA activators.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Structural Biology

Background:

  • Protein kinase R (PKR) is a crucial mediator in the interferon-induced antiviral defense pathway.
  • PKR activation involves autophosphorylation upon binding to double-stranded RNA (dsRNA).
  • The protein comprises an N-terminal dsRNA binding domain and a C-terminal kinase domain.

Purpose of the Study:

  • To elucidate the solution conformation of latent Protein kinase R (PKR).
  • To investigate the structural flexibility of PKR and its implications for function.

Main Methods:

  • Small-angle X-ray scattering (SAXS) was employed to study PKR structure in solution.
  • Small-angle neutron scattering (SANS) provided complementary structural information.
  • Guinier analysis and p(r) distance distribution functions were used to model PKR conformation.

Main Results:

  • SAXS/SANS data indicated a radius of gyration of approximately 35 Å for latent PKR.
  • The distance distribution function showed a peak near 30 Å with a tail extending to longer distances.
  • Structural models necessitated the inclusion of multiple compact and extended conformations for the interdomain linker regions, suggesting intrinsically unstructured regions.

Conclusions:

  • PKR possesses intrinsically unstructured regions within its interdomain linkers.
  • This structural flexibility likely facilitates productive dimerization upon interaction with diverse RNA activators.
  • The findings contribute to understanding the dynamic nature of PKR in antiviral signaling.