Project 6, APOBEC/AID family of proteins: In the absence of the HIV accessory protein Vif, virionencapsidated APOBEC3G (A3G) causes extensive C-to-U mutations, thereby damaging newly synthesized minus-strand viral DNA). it also physically blocks RTxn. These actions render the virus noninfectious. To understand A3G's activities at the atomic level, we will determine the structures of several proteins of the APOBEC/AID family, using standard solution NMR and X-ray crystallography approaches (see NMR and X-ray Core descriptions). All APOBEC/AID proteins are cytidine deaminases that contain Zri binding clusters and exhibit a high degree of primary sequence similarity, for one-domain as well as two-domain variants. Among all the APOBECs, A3G has received the most attention, given its ability to restrict HIV in a delta Vif background. The monomeric as well as dimeric models of A3G were created based on an A2 Xray structure that exhibited a tetrameric arrangement in the crystal in striking contrast to the X-ray findings, we recently uncovered that APOBEC2 (A2) is monomeric in solution, and we have prepared labeled protein for NMR structure determination. The anticipated structure will yield important information with respect to the validity of using A2 as a surrogate model for A3G. The great importance of high-resolution structural information for A3G compels us to continue our endeavor towards obtaining a bonafide A3G structure, however, we also will study the related APOBEC3A (A3A) protein, characterizing its structure and enzymatic activity at the atomic level. Altogether the A2, A3A and, possibly, A3G structures should fill a conspicuous gap in our understanding of cytidine deamination in the context of HIV biology.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Specialized Center (P50)
Project #
Application #
Study Section
Special Emphasis Panel (ZRG1-AARR-K)
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of Pittsburgh
United States
Zip Code
Gupta, Rupal; Lu, Manman; Hou, Guangjin et al. (2016) Dynamic Nuclear Polarization Enhanced MAS NMR Spectroscopy for Structural Analysis of HIV-1 Protein Assemblies. J Phys Chem B 120:329-39
Van Oss, S Branden; Shirra, Margaret K; Bataille, Alain R et al. (2016) The Histone Modification Domain of Paf1 Complex Subunit Rtf1 Directly Stimulates H2B Ubiquitylation through an Interaction with Rad6. Mol Cell 64:815-825
Perilla, Juan R; Gronenborn, Angela M (2016) Molecular Architecture of the Retroviral Capsid. Trends Biochem Sci 41:410-20
Sharaf, Naima G; Ishima, Rieko; Gronenborn, Angela M (2016) Conformational Plasticity of the NNRTI-Binding Pocket in HIV-1 Reverse Transcriptase: A Fluorine Nuclear Magnetic Resonance Study. Biochemistry 55:3864-73
Byeon, In-Ja L; Byeon, Chang-Hyeock; Wu, Tiyun et al. (2016) Nuclear Magnetic Resonance Structure of the APOBEC3B Catalytic Domain: Structural Basis for Substrate Binding and DNA Deaminase Activity. Biochemistry 55:2944-59
Saito, Akatsuki; Ferhadian, Damien; Sowd, Gregory A et al. (2016) Roles of Capsid-Interacting Host Factors in Multimodal Inhibition of HIV-1 by PF74. J Virol 90:5808-23
Ning, Jiying; Erdemci-Tandogan, Gonca; Yufenyuy, Ernest L et al. (2016) In vitro protease cleavage and computer simulations reveal the HIV-1 capsid maturation pathway. Nat Commun 7:13689
Rasheedi, Sheeba; Shun, Ming-Chieh; Serrao, Erik et al. (2016) The Cleavage and Polyadenylation Specificity Factor 6 (CPSF6) Subunit of the Capsid-recruited Pre-messenger RNA Cleavage Factor I (CFIm) Complex Mediates HIV-1 Integration into Genes. J Biol Chem 291:11809-19
Ramalho, Ruben; Rankovic, Sanela; Zhou, Jing et al. (2016) Analysis of the mechanical properties of wild type and hyperstable mutants of the HIV-1 capsid. Retrovirology 13:17
Oum, Yoon Hyeun; Desai, Tanay M; Marin, Mariana et al. (2016) Click labeling of unnatural sugars metabolically incorporated into viral envelope glycoproteins enables visualization of single particle fusion. J Virol Methods 233:62-71

Showing the most recent 10 out of 113 publications