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Quinn CM, Wang M, Fritz MP, Runge B, Ahn J, Xu C, Perilla JR, Gronenborn AM, Polenova T. Dynamic regulation of HIV-1 capsid interaction with the restriction factor TRIM5α identified by magic-angle spinning NMR and molecular dynamics simulations. Proc Natl Acad Sci U S A 2018; 115:11519-11524. [PMID: 30333189 PMCID: PMC6233135 DOI: 10.1073/pnas.1800796115] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The host factor protein TRIM5α plays an important role in restricting the host range of HIV-1, interfering with the integrity of the HIV-1 capsid. TRIM5 triggers an antiviral innate immune response by functioning as a capsid pattern recognition receptor, although the precise mechanism by which the restriction is imposed is not completely understood. Here we used an integrated magic-angle spinning nuclear magnetic resonance and molecular dynamics simulations approach to characterize, at atomic resolution, the dynamics of the capsid's hexameric and pentameric building blocks, and the interactions with TRIM5α in the assembled capsid. Our data indicate that assemblies in the presence of the pentameric subunits are more rigid on the microsecond to millisecond timescales than tubes containing only hexamers. This feature may be of key importance for controlling the capsid's morphology and stability. In addition, we found that TRIM5α binding to capsid induces global rigidification and perturbs key intermolecular interfaces essential for higher-order capsid assembly, with structural and dynamic changes occurring throughout the entire CA polypeptide chain in the assembly, rather than being limited to a specific protein-protein interface. Taken together, our results suggest that TRIM5α uses several mechanisms to destabilize the capsid lattice, ultimately inducing its disassembly. Our findings add to a growing body of work indicating that dynamic allostery plays a pivotal role in capsid assembly and HIV-1 infectivity.
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Affiliation(s)
- Caitlin M Quinn
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh, Pittsburgh, PA 15260
| | - Mingzhang Wang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh, Pittsburgh, PA 15260
| | - Matthew P Fritz
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh, Pittsburgh, PA 15260
| | - Brent Runge
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh, Pittsburgh, PA 15260
| | - Jinwoo Ahn
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh, Pittsburgh, PA 15260
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260
| | - Chaoyi Xu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716
| | - Juan R Perilla
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716;
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh, Pittsburgh, PA 15260
| | - Angela M Gronenborn
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh, Pittsburgh, PA 15260;
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716;
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh, Pittsburgh, PA 15260
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Lu M, Hou G, Zhang H, Suiter CL, Ahn J, Byeon IJ, Perilla JR, Langmead CJ, Hung I, Gor'kov PL, Gan Z, Brey W, Aiken C, Zhang P, Schulten K, Gronenborn AM, Polenova T. Dynamic allostery governs cyclophilin A-HIV capsid interplay. Proc Natl Acad Sci U S A 2015; 112:14617-22. [PMID: 26553990 DOI: 10.1073/pnas.1516920112] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Host factor protein Cyclophilin A (CypA) regulates HIV-1 viral infectivity through direct interactions with the viral capsid, by an unknown mechanism. CypA can either promote or inhibit viral infection, depending on host cell type and HIV-1 capsid (CA) protein sequence. We have examined the role of conformational dynamics on the nanosecond to millisecond timescale in HIV-1 CA assemblies in the escape from CypA dependence, by magic-angle spinning (MAS) NMR and molecular dynamics (MD). Through the analysis of backbone (1)H-(15)N and (1)H-(13)C dipolar tensors and peak intensities from 3D MAS NMR spectra of wild-type and the A92E and G94D CypA escape mutants, we demonstrate that assembled CA is dynamic, particularly in loop regions. The CypA loop in assembled wild-type CA from two strains exhibits unprecedented mobility on the nanosecond to microsecond timescales, and the experimental NMR dipolar order parameters are in quantitative agreement with those calculated from MD trajectories. Remarkably, the CypA loop dynamics of wild-type CA HXB2 assembly is significantly attenuated upon CypA binding, and the dynamics profiles of the A92E and G94D CypA escape mutants closely resemble that of wild-type CA assembly in complex with CypA. These results suggest that CypA loop dynamics is a determining factor in HIV-1's escape from CypA dependence.
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