LOW RESOLUTION STRUCTURES OF HIV-1 5' -UTR AND THE NATIVE DIMER

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This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. During the replication process, HIV-1 viruses selectively package two copies of their full-length unspliced RNA genomes from a cellular pool that contains a substantial excess of cellular and spliced viral RNAs. The reasons for the dimeric genome packaging and the mechanism for the recognition of its own RNAs still remain unclear. Understanding the genome packaging mechanism will be essential for the development of new anti-AIDS strategies. Recent in vivo studies have indicated that the full length HIV-1 5'-untranslated region (UTR) and upstream coding regions of the gag gene are responsible for efficient genome packaging. However, the difficulties in crystallization and the large molecular size (~110 kDa) has posed enormous difficulties for X-ray crystallography and NMR characterizations (due to the resonance overlap and peak broadening). Small angle X-ray scattering will provide valuable low resolution structural information for this large RNA.(Ref. 1-3) Comparing the monomeric and dimeric 5'-UTR conformations can provide insight on the conformational change involved upon genome packaging. Cation-dependent folding can further be investigated by SAXS. Besides, extensive genetic and virological studies indicate that the genome recognition is mediated by the viral Gag polyprotein nucleocapsid domain. Early studies have shown that NC protein binds tightly to the SL2 and SL3 stem loops (Kd ~ 140 nM) located in the 5'-UTR. (Ref. 4-6) The NC-RNA complex conformation and binding stoichemitry can be addressed by SAXS. Comparison of NC binding to monomeric and dimeric RNAs can be rationalized in terms of the selective packaging the dimeric RNA genome.