Retrovirus integration is catalyzed by the viral integrase (IN), which forms a tetrameric complex with both ends of the linear viral DNA genome and captures a cellular target DNA for concerted insertions of the viral DNA termini. The IN-DNA complex formed by HIV-1 IN is the target of a class of antiviral drugs called IN strand- transfer inhibitors. A better understanding of the IN-DNA interactions is therefore important for improving the clinically relevant anti-HIV drugs as well as designing next-generation IN inhibitors. The recent success in the structural studies of prototype foamy virus (PFV) IN-DNA complexes led to tremendous amount of insights into the retrovirus integration reaction. However, structural characterization of IN-DNA complexes from any other retrovirus systems by X-ray crystallography has remained elusive, leaving open the question as to how well the architecture of the IN-DNA complexes is conserved between distantly related retrovirus systems. We hypothesize that domain arrangement and IN-DNA interactions within the intasome, a nucleoprotein complex containing the tetramer of IN with the viral and target DNA molecules, are different between the canonical 3- domain IN including HIV-1 IN and the larger 4-domain PFV IN featuring an additional DNA-binding domain and longer inter-domain linkers. To address this hypothesis, we will determine crystal structures of the intasome complexes formed by the canonical 3-domain retroviral INs. Using a novel approach we have developed, crystals of the Rous sarcoma virus intasome suitable for structure determination have been obtained. We will further use our technique to pursue the crystal structure of a lentiviral intasome bound to the host co-factor LEDGF/p75. Our X-ray crystallographic analyses will provide the critically needed structural information to better understand the integration of HIV-1 and closely related retroviruses.

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Using X-ray crystallography, we will investigate the mechanisms by which HIV-1 and related retroviruses permanently integrate their genetic information into the infected host cell's genomic DNA. The information obtained through this research may help design new antiviral drugs to treat AIDS.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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AIDS Molecular and Cellular Biology Study Section (AMCB)
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Sakalian, Michael
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University of Minnesota Twin Cities
Schools of Arts and Sciences
United States
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Pandey, Krishan K; Bera, Sibes; Shi, Ke et al. (2017) A C-terminal ""Tail"" Region in the Rous Sarcoma Virus Integrase Provides High Plasticity of Functional Integrase Oligomerization during Intasome Assembly. J Biol Chem 292:5018-5030
Yin, Zhiqi; Shi, Ke; Banerjee, Surajit et al. (2016) Crystal structure of the Rous sarcoma virus intasome. Nature 530:362-6
Shaban, Nadine M; Shi, Ke; Li, Ming et al. (2016) 1.92 Angstrom Zinc-Free APOBEC3F Catalytic Domain Crystal Structure. J Mol Biol 428:2307-2316
Grandgenett, Duane P; Pandey, Krishan K; Bera, Sibes et al. (2015) Multifunctional facets of retrovirus integrase. World J Biol Chem 6:83-94
Shi, Ke; Carpenter, Michael A; Kurahashi, Kayo et al. (2015) Crystal Structure of the DNA Deaminase APOBEC3B Catalytic Domain. J Biol Chem 290:28120-30
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