This research involves determining the three dimensional solution structure(s) of RNA sequences from the 5'end of the HIV-1 genome and its protein complexes. The 5'end of the HIV genome has a domain called """"""""Psi locus"""""""". This region contains four stem loop motifs (SL1-4) and is a known binding site for Gag polyprotein. The HIV virus carries two copies of full length genomic RNA. These copies are non-covalently linked at a particularly region called the dimer linkage site. The RNA sequences within Psi site have been found to be responsible for proper dimerization of the HIV genome as well as efficient viral encapsidation. This is mediated through Gag protein interactions with Psi locus. To this end, we are engaged in determinig the structures of an RNA dimer containing the wild- type sequences of SL1 (stem loop-1) of Psi locus. Further, we plan to solve the structure of this RNA dimer complexed with Nucleocapsid (NC) protein, a subdomain of Gag polyprotein, which is a zinc finger domain. So far, we have made excellent progress in determining the structure of RNA dimer. Our research requires active use of molecular graphics resources available at the Computer Graphics Laboratory (CGL). We make use of MidasPlus and its peripheral programs to display molecular structures on almost a daily basis.
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