Cryo-EM structure of the HIV-1 Pol polyprotein provides insights into virion maturation

Harrison, Jerry Joe Ebow Kingsley; Passos, Dario Oliveira; Bruhn, Jessica F.; Bauman, J.D.; Tuberty, Lynda; DeStefano, Jeffrey J.; Ruiz, Francesc Xavier; Lyumkis, Dmitry; Arnold, Eddy

doi:10.1126/sciadv.abn9874

Cited by 12 publications

(18 citation statements)

References 63 publications

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“… 62 ). GagPol dimerization has been proposed to be driven by sequences in the RT and PR domains of GagPol ( 63 ) and GagPol dimers are less stable and less enzymatically active than mature PR dimers [( 64 , 65 ); see ref. 62 for review].…”

Section: Discussionmentioning

confidence: 99%

Neutral sphingomyelinase 2 is required for HIV-1 maturation

Waheed

Zhu

Agostino

et al. 2023

Proc. Natl. Acad. Sci. U.S.A.

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HIV-1 assembly occurs at the inner leaflet of the plasma membrane (PM) in highly ordered membrane microdomains. The size and stability of membrane microdomains is regulated by activity of the sphingomyelin hydrolase neutral sphingomyelinase 2 (nSMase2) that is localized primarily to the inner leaflet of the PM. In this study, we demonstrate that pharmacological inhibition or depletion of nSMase2 in HIV-1-producer cells results in a block in the processing of the major viral structural polyprotein Gag and the production of morphologically aberrant, immature HIV-1 particles with severely impaired infectivity. We find that disruption of nSMase2 also severely inhibits the maturation and infectivity of other primate lentiviruses HIV-2 and simian immunodeficiency virus, has a modest or no effect on nonprimate lentiviruses equine infectious anemia virus and feline immunodeficiency virus, and has no effect on the gammaretrovirus murine leukemia virus. These studies demonstrate a key role for nSMase2 in HIV-1 particle morphogenesis and maturation.

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Section: Discussionmentioning

confidence: 99%

Neutral sphingomyelinase 2 is required for HIV-1 maturation

Waheed

Zhu

Agostino

et al. 2023

Proc. Natl. Acad. Sci. U.S.A.

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“…The generation of the VBOF followed the methods described by Aller et al [17] Briefly, the process involved the following steps: (1) reference sequences of the HIV genome and proteins were obtained from the NCBI database, (2) the amino acids and dNTPs required to produce HIV units were estimated by multiplying each sequence by the reference copy number, [21][22][23] (3) the adenosine triphosphate (ATP) requirements of polymerizing amino acids were calculated by the metric that 4 ATPs and 1 PPi were needed for the formation of 1 peptide bond, and (4) the required amino acids, dNTPs, and ATPs were converted into mmol/g dray weight (DW) scale, and the reactions were created using Reaction function in COBRApy package.…”

Section: Vbof Constructionmentioning

confidence: 99%

Flux Balance Analysis Reveals Potential Anti–HIV-1 Metabolic Targets

Han,

Luo,

et al. 2024

Infect Dis Immun

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Background Human immunodeficiency virus type 1 (HIV-1) remains a persistent global health challenge. Therefore, a continuous exploration of novel therapeutic strategies is essential. A comprehensive understanding of how HIV-1 utilizes the cellular metabolism machinery for replication can provide insights into new therapeutic approaches. Methods In this study, we performed a flux balance analysis using a genome-scale metabolic model (GEM) integrated with an HIV-1 viral biomass objective function to identify potential targets for anti–HIV-1 interventions. We generated a GEM by integrating an HIV-1 production reaction into CD4+ T cells and optimized for both host and virus optimal states as objective functions to depict metabolic profiles of cells in the status for optimal host biomass maintenance or for optimal HIV-1 virion production. Differential analysis was used to predict biochemical reactions altered optimal for HIV-1 production. In addition, we conducted in silico simulations involving gene and reaction knock-outs to identify potential anti–HIV-1 targets, which were subsequently validated by human phytohemagglutinin (PHA) blasts infected with HIV-1. Results Differential analysis identified several altered biochemical reactions, including increased lysine uptake and oxidative phosphorylation (OXPHOS) activities in the virus optima compared with the host optima. In silico gene and reaction knock-out simulations revealed de novo pyrimidine synthesis, and OXPHOS could serve as potential anti–HIV-1 metabolic targets. In vitro assay confirmed that targeting OXPHOS using metformin could suppress the replication of HIV-1 by 56.6% (385.4 ± 67.5 pg/mL in the metformin-treated group vs. 888.4 ± 32.3 pg/mL in the control group, P < 0.001). Conclusion Our integrated host-virus genome-scale metabolic study provides insights on potential targets (OXPHOS) for anti-HIV therapies.

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“…However, it still could not resolve the structures of many proteins. For example, Harrison et al [13] published the protease (PR) and reverse transcriptase (RT) components of human immunodeficiency virus type-1 (HIV-1) Pol polyprotein using the cryo-EM method using in vitro expressed full-length Pol polyprotein. Integrase (IN) is largely not observed in the structures except for the first 49 amino acids 2 of 17 in the N-terminal domain (NTD) of IN identified via focused classification in the region expected.…”

Section: Introductionmentioning

confidence: 99%

“…Integrase (IN) is largely not observed in the structures except for the first 49 amino acids 2 of 17 in the N-terminal domain (NTD) of IN identified via focused classification in the region expected. The authors suggested that the cause is flexibility between RT and IN, and within the subdomains of IN [13].…”

Section: Introductionmentioning

confidence: 99%

“…In this study, we developed a novel workflow to predict the tertiary structure of HIV-1 Pol from the HIV-1 NL4.3 strain [27], which is a laboratory-adapted strain used in many laboratories, including our laboratory. Our HIV-1 Pol structure was built upon the published partial HIV-1 Pol structure mentioned above [13] with the addition of other immature domains modeled with relevant experimentally determined structures obtained from a publicly available database [1]. This HIV-1 Pol dimer structure is the first full-length HIV Pol tertiary structure and would provide researchers with a great base to investigate Gag-Pol autoprocessing and develop novel anti-HIV drugs.…”

Section: Introductionmentioning

confidence: 99%

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Modeling and Analysis of HIV-1 Pol Polyprotein as a Case Study for Predicting Large Polyprotein Structures

Hao,

Imamichi,

Chang

2024

IJMS

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Acquired immunodeficiency syndrome (AIDS) is caused by human immunodeficiency virus (HIV). HIV protease, reverse transcriptase, and integrase are targets of current drugs to treat the disease. However, anti-viral drug-resistant strains have emerged quickly due to the high mutation rate of the virus, leading to the demand for the development of new drugs. One attractive target is Gag-Pol polyprotein, which plays a key role in the life cycle of HIV. Recently, we found that a combination of M50I and V151I mutations in HIV-1 integrase can suppress virus release and inhibit the initiation of Gag-Pol autoprocessing and maturation without interfering with the dimerization of Gag-Pol. Additional mutations in integrase or RNase H domain in reverse transcriptase can compensate for the defect. However, the molecular mechanism is unknown. There is no tertiary structure of the full-length HIV-1 Pol protein available for further study. Therefore, we developed a workflow to predict the tertiary structure of HIV-1 NL4.3 Pol polyprotein. The modeled structure has comparable quality compared with the recently published partial HIV-1 Pol structure (PDB ID: 7SJX). Our HIV-1 NL4.3 Pol dimer model is the first full-length Pol tertiary structure. It can provide a structural platform for studying the autoprocessing mechanism of HIV-1 Pol and for developing new potent drugs. Moreover, the workflow can be used to predict other large protein structures that cannot be resolved via conventional experimental methods.

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Cryo-EM structure of the HIV-1 Pol polyprotein provides insights into virion maturation

Cited by 12 publications

References 63 publications

Neutral sphingomyelinase 2 is required for HIV-1 maturation

Neutral sphingomyelinase 2 is required for HIV-1 maturation

Flux Balance Analysis Reveals Potential Anti–HIV-1 Metabolic Targets

Modeling and Analysis of HIV-1 Pol Polyprotein as a Case Study for Predicting Large Polyprotein Structures

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