The HIV-1 nucleocapsid protein (NC) is a short, basic, nucleic acid binding protein with 2 zinc finger domains, each containing the invariant CCHC metal-ion binding motif. The mature protein (55 amino acid residues) is produced by proteolytic cleavage of the Gag precursor and is found in the interior of the virus particle, where it is tightly associated with genomic RNA. NC or the NC domain in Gag has multiple functions during the virus replication cycle, including genomic RNA packaging and virus assembly, primer placement on viral RNA, reverse transcription, and integration. Many of these functions rely on the nucleic acid chaperone activity of NC, i.e., the ability to catalyze nucleic acid conformational rearrangements that lead to the most thermodynamically stable structure. The details of how NC facilitates nucleic acid rearrangement are not completely understood. The proposed work uses a combination of biochemical assays and novel biophysical approaches to study a variety of oligonucleotide systems designed to improve our current understanding of the role of NC in various nucleic acid restructuring events that are critical for reverse transcription.
The specific aims of the proposed work are: (1) To probe the mechanism of HIV-1 NC-mediated TAR RNA/DNA annealing; (2) To probe the general mechanism of HIV-1 NC-mediated strand exchange reactions; and (3) To perform comparative studies with HTLV-1, RSV, and MLV NC proteins. The remarkable biological properties of NC and its central role in retrovirus replication make NC an attractive target for new HIV therapeutics. Studying other NC proteins from related retroviral systems will provide insights into the different ways these divergent NC proteins function. The detailed understanding of NC's nucleic acid binding and chaperone activities gained from these studies will facilitate the development of effective and safe anti-AIDS therapeutic strategies. Moreover, if common mechanisms, functions and interventions can be identified for all retroviral NC proteins, 1 could envision rapid control of newly emerging retroviruses, which are also likely to share these common features. ? ? ?
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