Comparison of the Global Structure and Dynamics of Native and Unmodified tRNA super(val)

The effects of post-transcriptional modifications on the structure and dynamics of Escherichia coli tRNA super(val) were studied by NMR spectroscopy. NMR chemical shift data and residual dipolar couplings were used to show that the local secondary and tertiary structures are very similar in native and unmodified tRNA super(val). Rigid body restrained molecular dynamics calculations showed that the global structure of tRNA is unchanged by the post-transcriptional modifications. Deuterium exchange NMR experiments were used to probe the dynamics and flexibility of native and unmodified tRNA super(val). A similar set of slowly exchanging (t sub(1/2) > 3 min) imino protons were observed in both tRNAs, but the rates of exchange for the slowest exchanging imino protons were similar to 20 times faster in unmodified than in native tRNA. These results demonstrate that the dynamics and flexibility of tRNA super(val), but not the local or global structure, are significantly affected by post-transcriptional modifications.