|
1
|
Ball KA, Chan LM, Stanley DJ, Tierney E, Thapa S, Ta HM, Burton L, Binning JM, Jacobson MP, Gross JD. Conformational Dynamics of the HIV-Vif Protein Complex. Biophys J 2019; 116:1432-1445. [PMID: 30961890 PMCID: PMC6486493 DOI: 10.1016/j.bpj.2019.03.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 02/27/2019] [Accepted: 03/02/2019] [Indexed: 12/29/2022] Open
Abstract
Human immunodeficiency virus-1 viral infectivity factor (Vif) is an intrinsically disordered protein responsible for the ubiquitination of the APOBEC3 (A3) antiviral proteins. Vif folds when it binds Cullin-RING E3 ligase 5 and the transcription cofactor CBF-β. A five-protein complex containing the substrate receptor (Vif, CBF-β, Elongin-B, Elongin-C (VCBC)) and Cullin5 (CUL5) has a published crystal structure, but dynamics of this VCBC-CUL5 complex have not been characterized. Here, we use molecular dynamics (MD) simulations and NMR to characterize the dynamics of the VCBC complex with and without CUL5 and an A3 protein bound. Our simulations show that the VCBC complex undergoes global dynamics involving twisting and clamshell opening of the complex, whereas VCBC-CUL5 maintains a more static conformation, similar to the crystal structure. This observation from MD is supported by methyl-transverse relaxation-optimized spectroscopy NMR data, which indicates that the VCBC complex without CUL5 is dynamic on the μs-ms timescale. Our NMR data also show that the VCBC complex is more conformationally restricted when bound to the antiviral APOBEC3F (one of the A3 proteins), consistent with our MD simulations. Vif contains a flexible linker region located at the hinge of the VCBC complex, which changes conformation in conjunction with the global dynamics of the complex. Like other substrate receptors, VCBC can exist alone or in complex with CUL5 and other proteins in cells. Accordingly, the VCBC complex could be a good target for therapeutics that would inhibit full assembly of the ubiquitination complex by stabilizing an alternate VCBC conformation.
Collapse
Affiliation(s)
- K Aurelia Ball
- Department of Chemistry, Skidmore College, Saratoga Springs, New York.
| | - Lieza M Chan
- Department of Chemistry, Skidmore College, Saratoga Springs, New York
| | - David J Stanley
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California
| | - Elise Tierney
- Department of Chemistry, Skidmore College, Saratoga Springs, New York
| | - Sampriti Thapa
- Department of Chemistry, Skidmore College, Saratoga Springs, New York
| | - Hai M Ta
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California
| | - Lily Burton
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California
| | - Jennifer M Binning
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California
| | - Matthew P Jacobson
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California
| | - John D Gross
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California.
| |
Collapse
|
|
3
|
Binning JM, Smith AM, Hultquist JF, Craik CS, Caretta Cartozo N, Campbell MG, Burton L, La Greca F, McGregor MJ, Ta HM, Bartholomeeusen K, Peterlin BM, Krogan NJ, Sevillano N, Cheng Y, Gross JD. Fab-based inhibitors reveal ubiquitin independent functions for HIV Vif neutralization of APOBEC3 restriction factors. PLoS Pathog 2018; 14:e1006830. [PMID: 29304101 PMCID: PMC5773222 DOI: 10.1371/journal.ppat.1006830] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Revised: 01/18/2018] [Accepted: 12/18/2017] [Indexed: 12/18/2022] Open
Abstract
The lentiviral protein Viral Infectivity Factor (Vif) counteracts the antiviral effects of host APOBEC3 (A3) proteins and contributes to persistent HIV infection. Vif targets A3 restriction factors for ubiquitination and proteasomal degradation by recruiting them to a multi-protein ubiquitin E3 ligase complex. Here, we describe a degradation-independent mechanism of Vif-mediated antagonism that was revealed through detailed structure-function studies of antibody antigen-binding fragments (Fabs) to the Vif complex. Two Fabs were found to inhibit Vif-mediated A3 neutralization through distinct mechanisms: shielding A3 from ubiquitin transfer and blocking Vif E3 assembly. Combined biochemical, cell biological and structural studies reveal that disruption of Vif E3 assembly inhibited A3 ubiquitination but was not sufficient to restore its packaging into viral particles and antiviral activity. These observations establish that Vif can neutralize A3 family members in a degradation-independent manner. Additionally, this work highlights the potential of Fabs as functional probes, and illuminates how Vif uses a multi-pronged approach involving both degradation dependent and independent mechanisms to suppress A3 innate immunity.
Collapse
Affiliation(s)
- Jennifer M. Binning
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California, United States of America
| | - Amber M. Smith
- Keck Advanced Microscopy Laboratory and Department of Biochemistry and Biophysics, University of California, San Francisco, California, United States of America
- Howard Hughes Medical Institute, University of California, San Francisco, California, United States of America
| | - Judd F. Hultquist
- J. David Gladstone Institutes, San Francisco, California, United States of America
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, United States of America
- California Institute for Quantitative Biosciences, QB3, University of California, San Francisco, San Francisco, California, United States of America
| | - Charles S. Craik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California, United States of America
| | - Nathalie Caretta Cartozo
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California, United States of America
| | - Melody G. Campbell
- Keck Advanced Microscopy Laboratory and Department of Biochemistry and Biophysics, University of California, San Francisco, California, United States of America
- Howard Hughes Medical Institute, University of California, San Francisco, California, United States of America
| | - Lily Burton
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California, United States of America
| | - Florencia La Greca
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California, United States of America
| | - Michael J. McGregor
- J. David Gladstone Institutes, San Francisco, California, United States of America
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, United States of America
- California Institute for Quantitative Biosciences, QB3, University of California, San Francisco, San Francisco, California, United States of America
| | - Hai M. Ta
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California, United States of America
| | - Koen Bartholomeeusen
- Department of Medicine, University of California, San Francisco, California, United States of America
- Department of Microbiology, University of California, San Francisco, California, United States of America
- Department of Immunology, University of California, San Francisco, California, United States of America
| | - B. Matija Peterlin
- Department of Medicine, University of California, San Francisco, California, United States of America
- Department of Microbiology, University of California, San Francisco, California, United States of America
- Department of Immunology, University of California, San Francisco, California, United States of America
| | - Nevan J. Krogan
- J. David Gladstone Institutes, San Francisco, California, United States of America
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, United States of America
- California Institute for Quantitative Biosciences, QB3, University of California, San Francisco, San Francisco, California, United States of America
| | - Natalia Sevillano
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California, United States of America
| | - Yifan Cheng
- Keck Advanced Microscopy Laboratory and Department of Biochemistry and Biophysics, University of California, San Francisco, California, United States of America
- Howard Hughes Medical Institute, University of California, San Francisco, California, United States of America
| | - John D. Gross
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California, United States of America
| |
Collapse
|