HIV requires the host cell machinery for replication. Many complexes hijacked by HIV have been identified, but structures are known in only a few cases. The HARC Center is taking a broad systems-to-structure approach to this problem, having identified and validated new host complexes through a comprehensive proteomics effort. Primary biological aims of the Center are to achieve comprehensive structural pictures of: (1) how the accessory proteins Vif, Vpu, Vpr, and the viral protease PR disarm host defenses and circumvent viral restriction via degradation pathways, and (2) how the regulatory proteins Tat and Rev hijack the host transcription and RNA trafficking machinery to express and package viral RNAs. There is growing evidence that HIV accessory proteins primarily target host antiviral restriction factors for destruction. For Vif, we will determine the structures of the E3 ligase complex and interactions with APOBEC, and evaluate the functional roles of the CBF? cofactor and post-translational modifications (PTMs). For Vpu, we will determine the structures of restriction factor complexes and map effects of Vpu on ubiquitination. For Vpr, we will validate new host interactions and mechanisms and assemble complexes for structure determination. For PR, we will determine the structures and functions of new host target complexes and measure the levels of PR activity during infection. The regulatory proteins Tat and Rev hijack host transcription and RNA export machineries. For Tat, we will determine the structures of newly discovered AFF4 elongation complexes, and characterize other host factors, PTMs, and inhibitory 7SK snRNP complexes. For Rev, we will determines the structures of Rev-RRE nuclear export complexes, map viral RNA structures, and characterize the roles of new host proteins in post export functions. The HARC Center also relies on technology innovation from four cores. The EM Core will develop methods to determine structures of membrane protein complexes, and use Fabs to solve the structures of small HIV-host complexes. The Proteomics Core will extend mass spectrometry analyses to host protein complexes and map HIV-dependent host PTMs. The Computational Core will develop methods to characterize allostery and detailed models to study PTMs. The Virology Core will measure effects of new host interactions on HIV replication and coupled activities of Tat and Rev. The individual projects and technologies depend critically on an extensive network of collaborators, which will be expanded through a Collaborative Opportunity Fund.

Public Health Relevance

Existing anti-HIV therapeutics have extended the life expectancy of infected individuals, however major limitations remain, including drug resistance. By determining structures of key HIV accessory and regulatory complexes, we will achieve a more complete molecular understanding of how the virus hijacks the host cell machinery, and also identify new targets for therapeutic intervention in the continuing battle against AIDS.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Specialized Center (P50)
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Study Section
Special Emphasis Panel (ZRG1-AARR-K (50))
Program Officer
Sakalian, Michael
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University of California San Francisco
Schools of Medicine
San Francisco
United States
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Davis, Zoe H; Verschueren, Erik; Jang, Gwendolyn M et al. (2015) Global mapping of herpesvirus-host protein complexes reveals a transcription strategy for late genes. Mol Cell 57:349-60
Lu, Huasong; Li, Zichong; Xue, Yuhua et al. (2014) AFF1 is a ubiquitous P-TEFb partner to enable Tat extraction of P-TEFb from 7SK snRNP and formation of SECs for HIV transactivation. Proc Natl Acad Sci U S A 111:E15-24
Lang, P Therese; Holton, James M; Fraser, James S et al. (2014) Protein structural ensembles are revealed by redefining X-ray electron density noise. Proc Natl Acad Sci U S A 111:237-42
Monroe, Kathryn M; Yang, Zhiyuan; Johnson, Jeffrey R et al. (2014) IFI16 DNA sensor is required for death of lymphoid CD4 T cells abortively infected with HIV. Science 343:428-32
Ren, Xuefeng; Park, Sang Yoon; Bonifacino, Juan S et al. (2014) How HIV-1 Nef hijacks the AP-2 clathrin adaptor to downregulate CD4. Elife 3:e01754
Schulze-Gahmen, Ursula; Lu, Huasong; Zhou, Qiang et al. (2014) AFF4 binding to Tat-P-TEFb indirectly stimulates TAR recognition of super elongation complexes at the HIV promoter. Elife 3:e02375
Fujinaga, Koh; Luo, Zeping; Peterlin, B Matija (2014) Genetic analysis of the structure and function of 7SK small nuclear ribonucleoprotein (snRNP) in cells. J Biol Chem 289:21181-90
Hu, Shenshen; Sharma, Sudhir C; Scouras, Alexander D et al. (2014) Extremely elevated room-temperature kinetic isotope effects quantify the critical role of barrier width in enzymatic C-H activation. J Am Chem Soc 136:8157-60
Gable, Jonathan E; Lee, Gregory M; Jaishankar, Priyadarshini et al. (2014) Broad-spectrum allosteric inhibition of herpesvirus proteases. Biochemistry 53:4648-60
Holton, James M; Classen, Scott; Frankel, Kenneth A et al. (2014) The R-factor gap in macromolecular crystallography: an untapped potential for insights on accurate structures. FEBS J 281:4046-60

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