In the case of AIDS virus HIV-1, like other retroviruses, genetic material is packed in virus particles as a diploid RNA. During formation of viruses in host cell, each virus specifically encapsulates two identical copies of genomic RNA. The specificity of this process is regulated by certain sequences on RNA genome and their interaction with Nucleocapsid portion of Polygag protein. My research involves determining the three dimensional solution structures(s) of RNA sequences from the dimerization domain of HIV-1 genomic RNA and its protein complexes. The 5'-end of the HIV-1 genome possesses a domain called """"""""Psi locus"""""""" which contains four stem loop motifs. These stem loop structures are known to bind with Gag protein and are instrumental in efficient dimerization and packaging of viral RNA. In order to understand the mechanism of this recognition and function, I have solved the high resolution NMR structure of dimer RNA complex formed by two copies of stem-loop-1 (SL1) of Psi locus. Structure presents unique interactions of certain mutationally indispensable residues, suggesting a specific mode of nucleocapsid binding to the dimer. Work is now progressing towards solving the protein complex of SL-1 RNA dimer. My research involves an active use of molecular graphic resources available at the Computer Graphic Laboratory, on almost daily basis. I make rigorous use of MidasPlus and its peripheral programs to display and render molecular structures.
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