My group uses a wide variety of chemical and biophysical approaches to answer fundamental questions focusing on nucleic acids (RNA and DNA) and proteins that are involved in translation of the genetic code and viral replication. Here, we describe the current interests of our retrovirus subgroup members.
Nucleic Acid-Protein Interactions in HIV
During the life cycle of HIV, its RNA genome must be converted into DNA. This conversion is catalyzed by reverse transcriptase, an enzyme that uses a specific host cell tRNALys molecule as a primer. The process by which HIV selects and uses a specific primer tRNA is not well understood, but we have recently shown that human lysyl-tRNA synthetase (LysRS) is also packaged into HIV and appears to be a critical factor in specific tRNA packaging. Ongoing work is aimed at elucidating the molecular interactions between human LysRS and HIV proteins. Figure 3 illustrates the propsed tRNA packaging complex for HIV-1. In vivo, the tRNA primer and the HIV RNA genome must be unwound and annealed together before reverse transcription can be initiated. The annealing process is mediated by the HIV nucleocapsid protein (NC), a nucleic acid “chaperone” protein that facilitates nucleic acid rearrangements (Figure 4). We have reconstituted in vitro systems that closely mimic several steps of the reverse transcription process in HIV to elucidate the mechanism of NCs chaperone funtion. Experimental approaches we are currently using to elucidate key nucleic acid-protein interactions in this system include fluorescence resonance energy transfer (FRET), chemical footprinting, and single molecule DNA stretching.