Xinlei Wang, Lela Vukovic, Hye Ran Koh, Klaus Schulten, and Sua Myong.
Dynamic profiling of double-stranded RNA binding proteins.
Nucleic Acids Res., 43:7566-7576, 2015.
(PMC: PMC4551942)
WANG2015
Double-stranded (ds) RNA is a key player in numerous biological activities in cells,
including RNA interference, anti-viral immunity and mRNA transport. The class of
proteins responsible for processing dsRNA is termed double-stranded RNA binding
proteins (dsRBP). However, little is known about the molecular mechanisms underlying
the interaction between dsRBPs and dsRNA. Here we examined four dsRBPs, ADAD2,
TRBP, Staufen 1 and ADAR1 on six dsRNA substrates that vary in length and secondary
structure. We combined single molecule pull-down (SiMPull), single molecule protein-
induced fluorescence enhancement (smPIFE) and molecular dynamics (MD) simulations
to investigate the dsRNA-dsRBP interactions. Our results demonstrate that despite the
highly conserved dsRNA binding domains, the dsRBPs exhibit diverse substrate
specificities and dynamic properties when in contact with different RNA substrates. While
TRBP and ADAR1 have a preference for binding simple duplex RNA, ADAD2 and
Staufen1 display higher affinity to structured RNA substrates. Upon interaction with RNA
substrates, TRBP and Staufen1 exhibit dynamic sliding whereas two deaminases ADAR1
and ADAD2 mostly remain immobile when bound. MD simulations provide a detailed
atomic interaction map that is largely consistent with the affinity differences observed
experimentally. Collectively, our study highlights the diverse nature of substrate
specificity and mobility exhibited by dsRBPs that may be critical for their cellular
function.
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