Over the past 3 1/2 years we have (i) determined that metal coordination properties and structures of peptides corresponding to the N-and C- terminal CCHC-type zinc finger domains of the HIV-1 nucleocapsid (NC) protein CCHC=Cys-X2-Cys-His-X4-Cys; X=variable amino acid, (ii) demonstrated that the CCHC arrays are populated with zinc in intact virions, providing direct evidence for the physiological relevance of CCHC zinc nucleocapsid protein, (iv) identified a sequenced-dependent single-stranded nucleic acid binding mode for the N-terminal CCHC zinc finger and determined the structure of a zinc finger-nucleic acid complex (v) identified a new class of anti-HIV agents that function by ejecting zinc from the NC zinc fingers. Outstanding questions include: What are the nucleotide binding properties of the C-terminal HIV-1 NC zinc finger? (In view of substantial differences in the surface topologies of the N- and C-terminal NC zinc fingers, the binding properties should be significantly different). What are the similarities and/or differences between DNA and RNA binding to NC zinc fingers? What is the structure of intact NC when bound to nucleic acid, and in particular, what is the conformation (and potential contribution to nucleotide binding) of the """"""""flexible"""""""" linker region"""""""" Finally, R-NO nitroso compounds with anti- retroviral properties eject zinc preferentially from CCHC-type zinc fingers, and what are the intrinsic chemical factors that lead to different rates of zinc ejection by these nucleic acid interactive properties of synthetic NC zinc fingers including studies of both DNA and RNA binding recombinant HIV-1 NC protein, (3) structural studies of the NC proteins from other retroviruses, including human T-cell leukemia virus type-1 (HTLV-1, which contains an unusual poly-proline linker domain) and simian immunodeficiency virus (SIV; a primary retrovirus model used for vaccine and drug development), and (4) studies of the mechanism of HIV-1 inhibition by zinc-ejecting C-nitroso agents. Knowledge of the 3D structural details and biophysical properties of retroviral NC proteins is important for understanding their functions, and will facilitate the development of vaccines and new chemotherapeutic approaches for the control of retroviral disease, including leukemia and AIDS.
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