Immature HIV-1 assembles from Gag dimers leaving partial hexamers at lattice edges as potential substrates for proteolytic maturation

Tan, Aaron; Pak, Alexander J.; Morado, Dustin R.; Voth, Gregory A.; Briggs, John

doi:10.1073/pnas.2020054118

Cited by 45 publications

(60 citation statements)

References 53 publications

(78 reference statements)

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“…2d), indicating the complete hexagons are not assembly units of HIV. In concert with this observation, a recent study shows the Gag dimers are the basic assembly units of the HIV-1 particle 28 . These protrusions could be Gag dimers and are prone to structural changes during proteolytic cleavage .…”

Section: Application To Virus Tomogramsmentioning

confidence: 70%

Isotropic Reconstruction of Electron Tomograms with Deep Learning

Liu

Zhang

Wang

et al. 2021

Preprint

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Cryogenic electron tomography (cryoET) allows visualization of cellular structures in situ. However, anisotropic resolution arising from the intrinsic missing-wedge problem has presented major challenges in visualization and interpretation of tomograms. Here, we have developed IsoNet, a deep learning-based software package that iteratively reconstructs the missing-wedge information and increases signal-to-noise ratio, using the knowledge learned from raw tomograms. Without the need for sub-tomogram averaging, Isonet generates tomograms with significantly reduced resolution anisotropy. Applications of IsoNet to three representative types of cryoET data demonstrate greatly improved structural interpretability: resolving lattice defects in immature HIV particles, establishing architecture of the paraflagellar rod in Eukaryotic flagella, and identifying heptagon-containing clathrin cages inside a neuronal synapse of cultured cells. Therefore, by overcoming two fundamental limitations of cryoET, IsoNet enables functional interpretation of cellular tomograms without sub-tomogram averaging. Its application to high-resolution cellular tomograms should also help identify differently oriented complexes of the same kind for near-atomic resolution sub-tomogram averaging.

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Section: Application To Virus Tomogramsmentioning

confidence: 70%

Isotropic Reconstruction of Electron Tomograms with Deep Learning

Liu

Zhang

Wang

et al. 2021

Preprint

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“…The escape mutants reduce six-fold symmetry throughout the 6HB, which is partially recovered by BVM in particular cases. Our free energy calculations demonstrate that loss of six-fold symmetry facilitates helical uncoiling, which precedes proteolytic cleavage (19,22). Consequently, the efficacy of BVM is due to additional resistance to symmetry loss.…”

Section: Discussionmentioning

confidence: 81%

“…More recently, cryo-EM and MD analysis suggested that the edges of the fissures within immature HIV-1 capsid particles expose incomplete Gag hexamers, which could be the potential substrates for protease cleavage (22). This would imply that only the protomers within incomplete 6HBs may be in a dynamic helix-coil equilibrium.…”

Section: Introductionmentioning

confidence: 99%

Preservation of HIV-1 Gag helical bundle symmetry by bevirimat is central to maturation inhibition

Pak

Purdy

Yeager

et al. 2021

Preprint

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The assembly and maturation of human immunodeficiency virus type-1 (HIV-1) requires proteolytic cleavage of the Gag polyprotein. The rate-limiting step resides at the junction between the capsid protein CA and spacer peptide 1, which assembles as a six-helix bundle (6HB). bevirimat (BVM), the first-in-class maturation inhibitor drug, targets the 6HB and impedes proteolytic cleavage, yet the molecular mechanisms of its activity, and relatedly, the escape mechanisms of mutant viruses, remain unclear. Here, we employed extensive molecular dynamics (MD) simulations and free energy calculations to quantitatively investigate molecular structure-activity relationships, comparing wild-type and mutant viruses in the presence and absence of BVM and inositol hexakisphosphate (IP6), an assembly cofactor. Our analysis shows that the efficacy of BVM is directly correlated with preservation of six-fold symmetry in the 6HB, which exists as an ensemble of structural states. We identified two primary escape mechanisms, and both lead to loss of symmetry, thereby facilitating helix uncoiling to aid access of protease. Our findings also highlight specific interactions that can be targeted for improved inhibitor activity and support the use of MD simulations for future inhibitor design.

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“…Curiously, sequence alignments revealed little conservation of putative L-Domains across viruses, suggesting that the model for ALIX recruitment may only occur in select herpesvirus nuclear egress pathways. Perhaps in cases of ESCRT-III dependent nuclear egress, an edge of the NEC containing the L-Domain sequence is exposed to the nucleoplasm to be recognized for ALIX-mediated membrane budding and scission, much like how HIV-1 Gag recruits ALIX to the plasma membrane [71]. Although this model places the L-Domain of the NEC proximal to the nuclear envelope, this proposed mechanism is not unlike the recruitment of ESCRTs seen for beta-retroviruses and spuma-retroviruses where ESCRT binding is predicted to occur close to the plasma membrane [72,73].…”

Section: The Necs Of Herpesviruses Form Gag-like Assemblies That Interact With Alix and Are Required For Efficient Nuclear Egressmentioning

confidence: 99%

When in Need of an ESCRT: The Nature of Virus Assembly Sites Suggests Mechanistic Parallels between Nuclear Virus Egress and Retroviral Budding

Rose

2021

Viruses

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The proper assembly and dissemination of progeny virions is a fundamental step in virus replication. As a whole, viruses have evolved a myriad of strategies to exploit cellular compartments and mechanisms to ensure a successful round of infection. For enveloped viruses such as retroviruses and herpesviruses, acquisition and incorporation of cellular membrane is an essential process during the formation of infectious viral particles. To do this, these viruses have evolved to hijack the host Endosomal Sorting Complexes Required for Transport (ESCRT-I, -II, and -III) to coordinate the sculpting of cellular membrane at virus assembly and dissemination sites, in seemingly different, yet fundamentally similar ways. For instance, at the plasma membrane, ESCRT-I recruitment is essential for HIV-1 assembly and budding, while it is dispensable for the release of HSV-1. Further, HSV-1 was shown to recruit ESCRT-III for nuclear particle assembly and egress, a process not used by retroviruses during replication. Although the cooption of ESCRTs occurs in two separate subcellular compartments and at two distinct steps for these viral lifecycles, the role fulfilled by ESCRTs at these sites appears to be conserved. This review discusses recent findings that shed some light on the potential parallels between retroviral budding and nuclear egress and proposes a model where HSV-1 nuclear egress may occur through an ESCRT-dependent mechanism.

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Immature HIV-1 assembles from Gag dimers leaving partial hexamers at lattice edges as potential substrates for proteolytic maturation

Cited by 45 publications

References 53 publications

Isotropic Reconstruction of Electron Tomograms with Deep Learning

Isotropic Reconstruction of Electron Tomograms with Deep Learning

Preservation of HIV-1 Gag helical bundle symmetry by bevirimat is central to maturation inhibition

When in Need of an ESCRT: The Nature of Virus Assembly Sites Suggests Mechanistic Parallels between Nuclear Virus Egress and Retroviral Budding

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