Intermediate Rate Atomic Trajectories of RNA by Solid State NMR Spectroscopy

Abstract

Many RNAs undergo large conformational changes in response to the binding of proteins and small molecules. However, when RNA functional dynamics occur in the ns-μs time scale they become invisible to traditional solution NMR relaxation methods. Residual dipolar couplings methods have revealed the presence of extensive ns-μs domain motions in HIV-1 TAR RNA, but this technique lacks information on the rates of motions. We have used solid-state deuterium NMR to quantitatively describe trajectories of key residues in TAR by exploiting the sensitivity of this technique to motions that occur in the ns-μs regime. Deuterium lineshape and relaxation data were used to model motions of residues within the TAR binding interface. The resulting motional models indicate that two functionally essential bases within the single stranded bulge sample both the free and Tat-bound conformations on the microsecond timescale in the complete absence of the protein. Thus, our results strongly support a conformational capture mechanism for recognition: the protein does not induce a new RNA structure, but instead captures an already-populated conformation.