NMR Studies of Retroviral Nucleic Acid Binding Proteins

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DESCRIPTION (Provided by the applicant): During the past 3-1/2 years we (i) identified the stem loops of the HIV-1 Psi-RNA packaging signal that have high affinities for the nucleocapsid (NC) protein; (ii) determined the structures of NC complexes with HIV-1 Psi-site stem loops SL2 and SL3; (iii) established the functional roles of the HIV-1 CCHC zinc knuckles and their conserved amino acid residues; (iv) demonstrated that SL4 does not bind tightly to NC, as had previously been reported, and proposed a new role for this essential packaging element; and (v) discovered a novel three dimensional fold in the C-terminal zinc knuckle of the Mouse Mammary Tumor Virus (MMTV) NC protein. In addition, we recently (vi) developed a method for overproduction of the recombinant NC protein from the Moloney Murine Leukemia Virus (MLV), which is the most widely used vector in human gene therapy trials, and (vii) identified the minimal portion of MLV Psi-site that is necessary for high-affinity NC binding. Having completed studies of NC binding to isolated stem loops, we now intend to study NC interactions with the intact Psi-sites of MLV and HIV- 1. High quality preliminary NMR spectra have been obtained for the 102 nucleotide NC-binding domain of the MLV Psi-site (>70 percent assigned at the time of submission), and numerous intermolecular NOES have been observed in preliminary NMR data obtained for its complex with NC. Promising preliminary 3D NMR data have also been obtained for the intact, 116 nucleotide HIV-1 Psi- site, indicating that structural studies of this 72.4 kDa symmetrical dimer are also feasible. Studies of RNAs of 100 nucleotides or larger are technically more challenging than our previous studies with relatively small RNA stem loops. However, the potential payoff is substantially greater, and promises to provide the first detailed structural information for the recognition complexes that lead to the specific packaging of retroviral genomes. Such knowledge should not only facilitate the development of approaches for the treatment of AIDS and cancer, but should also assist in the development of MLV as a more effective agent for the therapeutic delivery of human genes.