A 35-base RNA stem-loop called SL-1, located near the 5 ' end of the HIV genome, mediates several functions crucial for viral assembly, and so is a potential target for antiviral therapy. By binding the HIV Gag protein, SL1 forms part of the packaging signal that targets genomic RNA into virions. Contact between SL1 elements in a pair of HIV RNAs (through an initial """"""""kissing-loop"""""""" complex which then converts to a linear duplex) also initiates genomic dimerization--a process that is facilitated by Gag and is essential for full infectivity. All biological activities of SL1 depend upon its three- dimensional structure, whose exact nature is unknown. The PIs laboratory has used NMR spectroscopy to examine a truncated form of SL1 in its kissing-loop and linear duplex conformations. They have obtained excellent NMR spectra on the RNA. They propose to solve the structures of the monomer and both dimer forms of this RNA, and so to obtain the first high- resolution images of a retroviral dimer interface. Guided by these structures, they will systematically mutagenize SL1 to map the molecular contacts needed to stabilize each conformational state. They also propose to use real-time NMR kinetic studies to study the sequence of events in SL1 dimerization. Multidimensional NMR on heteronuclear labeled RNA will be used to solve the structure of a full-length SL1 analogue that is fully competent for Gag binding as well as dimerization. Studies of this RNA in complex with unlabeled Gag protein will reveal the structural basis for Gag recognition and the mechanism by which Gag facilitates SL1-mediated dimerization. Results of these studies may provide a basis for rational design of new antivirals that target the SL1/Gag interaction.

Agency
National Institute of Health (NIH)
Institute
National Institute of Allergy and Infectious Diseases (NIAID)
Type
Research Project (R01)
Project #
5R01AI036636-05
Application #
6124373
Study Section
AIDS and Related Research Study Section 4 (ARRD)
Program Officer
Plaeger, Susan F
Project Start
1994-12-01
Project End
2001-03-31
Budget Start
1999-12-01
Budget End
2001-03-31
Support Year
5
Fiscal Year
2000
Total Cost
$200,137
Indirect Cost
Name
University of California San Francisco
Department
Pathology
Type
Schools of Medicine
DUNS #
073133571
City
San Francisco
State
CA
Country
United States
Zip Code
94143
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

Showing the most recent 10 out of 14 publications