Poster abstracts

Poster number 26 submitted by Charles Fisher

Conformational Dynamics of HIV-2 TAR by NMR

Charles Fisher (Department of Chemistry and Biophysics Research Division), Qi Zhang (Department of Chemistry and Biophysics Research Division), Eric Watt (Department of Chemistry and Biophysics Research Division), Hashm M. Al-Hashimi (Department of Chemistry and Biophysics Research Division)

Abstract:
We used a domain elongation strategy and Nuclear Magnetic Resonance (NMR) spin relaxation and residual dipolar coupling methods to examine how shortening the length of the TAR RNA bulge linker from three (HIV-1 form) to two (HIV-2 form) residues affects its structural dynamics and corresponding ability to adaptively bind diverse targets. We observe up to ~65% decrease in the amplitude of inter-domain motions occurring at both nanosecond and micro-millisecond timescales in HIV-2 TAR as compared to HIV-1 TAR. The reduced domain motional amplitudes originate from decreased local flexibility occurring at nanosecond timescales at the backbone of bulge and neighboring stem residues. In contrast, increased flexibility is observed in the nucleobases of HIV-2 TAR which can be explained by looping out of the bulge residues owing to greater coaxial stacking of the two domains. Analysis of RDCs shows that while HIV-1 TAR can be modeled as inter-converting among its previously reported bound structures, only a subset of the bound conformers are needed to re-construct the corresponding dynamical ensemble of HIV-2 TAR. Remarkably, the HIV-2 TAR conformers are precisely those that have the most linear inter-domain alignments. These results indicate that HIV-2 TAR is less predisposed to adaptively form bent conformations that can be formed by HIV-1 TAR. Binding data in support of this hypothesis will be presented.

Keywords: RNA dynamics, adaptive recognition, NMR