: A 35-base RNA stem-loop called SL1, located near the 5' end of the HIV-1 genome, mediates several functions crucial for viral assembly, and so is a potential new target for antiviral therapy. By binding the nucleocapsid (NCp7) portion of the HIV Gag protein, SL1 forms part of the packaging signal that targets genomic RNA into virions. Contact between SL1 loops in a pair of H1V RNAs (forming an initial """"""""kissing-loop"""""""" complex that then refolds into a linear duplex) also initiates genomic dimerization - a process that is facilitated by NCp7 binding and is essential for full infectivity. All biological activities of SL1 depend on its three-dimensional structure. During the previous funded period, we used nuclear magnetic resonance (NMR) spectroscopy to solve the structure of a truncated, 23-base SL1 derivative in both its kissing-loop and linear forms the first such structures to be solved for any retrovirus. Using heteronuclear labeling and multidimensional NMR, we now propose to solve the corresponding structures of full-length, authentic SL1, which contains additional features that are biologically important. By determining the SL1 monomer, kissing-loop, and linear structures, we seek to understand the remarkable efficiency with which SL1 dimerizes and the chemical features that stabilize each successive conformation. We will also determine the structures and dynamics of complexes formed when HIV NCp7 protein binds each RNA conformer, revealing the exact molecular contacts involved and the mechanism by which NCp7 facilitates refolding of SL1 and other nucleic acids. The validity of our structural insights will then be tested through targeted mutagenesis of SL1 and NCp7. Real-time NMR will be used to dissect the sequence of events that occur at individual bases in SL1 as it dimerizes and then linearizes in vitro. In addition, we will solve the complex formed by NCp7 with a heterologous, monomeric RNA ligand (aptamer) that binds with higher affinity than SL1, to identify features that account for its tight binding and could be exploited in rational drug design. Results of these studies will provide a basis for discovering new antivirals that target the SL1/NCp7 interaction.

National Institute of Health (NIH)
National Institute of Allergy and Infectious Diseases (NIAID)
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Special Emphasis Panel (ZRG1-AARR-1 (01))
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Sharma, Opendra K
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Emory University
Schools of Medicine
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Mujeeb, Anwer; Ulyanov, Nikolai B; Georgantis, Stefanos et al. (2007) Nucleocapsid protein-mediated maturation of dimer initiation complex of full-length SL1 stemloop of HIV-1: sequence effects and mechanism of RNA refolding. Nucleic Acids Res 35:2026-34
Regan, John F; Liang, Yuying; Parslow, Tristram G (2006) Defective assembly of influenza A virus due to a mutation in the polymerase subunit PA. J Virol 80:252-61
Ulyanov, Nikolai B; Mujeeb, Anwer; Du, Zhihua et al. (2006) NMR structure of the full-length linear dimer of stem-loop-1 RNA in the HIV-1 dimer initiation site. J Biol Chem 281:16168-77
Ly, Hinh; Schertzer, Mike; Jastaniah, Wasil et al. (2005) Identification and functional characterization of 2 variant alleles of the telomerase RNA template gene (TERC) in a patient with dyskeratosis congenita. Blood 106:1246-52
Ly, Hinh; Calado, Rodrigo T; Allard, Paulette et al. (2005) Functional characterization of telomerase RNA variants found in patients with hematologic disorders. Blood 105:2332-9
Ly, Hinh; Xu, Lifeng; Rivera, Melissa A et al. (2003) A role for a novel 'trans-pseudoknot' RNA-RNA interaction in the functional dimerization of human telomerase. Genes Dev 17:1078-83
Ly, Hinh; Blackburn, Elizabeth H; Parslow, Tristram G (2003) Comprehensive structure-function analysis of the core domain of human telomerase RNA. Mol Cell Biol 23:6849-56
Clever, J L; Taplitz, R A; Lochrie, M A et al. (2000) A heterologous, high-affinity RNA ligand for human immunodeficiency virus Gag protein has RNA packaging activity. J Virol 74:541-6
Mujeeb, A; Parslow, T G; Zarrinpar, A et al. (1999) NMR structure of the mature dimer initiation complex of HIV-1 genomic RNA. FEBS Lett 458:387-92
Clever, J L; Eckstein, D A; Parslow, T G (1999) Genetic dissociation of the encapsidation and reverse transcription functions in the 5' R region of human immunodeficiency virus type 1. J Virol 73:101-9

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