This research involves determining the solution structure of RNA binding proteins from HIV-1 and the structure of subsequent RNA domains. The HIV lifestyle depends absolutely on certain sequence specific interactions between virally encoded proteins and viral RNA. Each of these interactions is a promising, but as yet unexploited, target for HIV therapy. We are targeting the Tat protein interaction with TAR element in HIV1 genomic RNA to explain the mode of interaction of these segments. We are also looking into the phenomenon of dimerization of HIV genome. We are using combined approaches of molecular genetics and nuclear magnetic resonance (NMR) followed by molecular modelling to probe the structural basis of these interactions. So, far, we have established the structure of a chimeric peptide which contains the activation domain from Tat protein and binds with TAR RNA sequence. Recently we have proposed a model of this interaction. 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 an almost daily basis.
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