HIV-2 Immature Particle Morphology Provides Insights into Gag Lattice Stability and Virus Maturation

Talledge, Nathaniel; Yang, Huixin; Shi, Ke; Coray, Raffaele; Yu, Guichuan; Arndt, William G.; Meng, Shuyu; Baxter, Gloria C; Mendonça, L.G.D.; Castaño-Díez, Daniel; Aihara, Hideki; Mansky, Louis M.; Zhang, Wei

doi:10.1016/j.jmb.2023.168143

Cited by 3 publications

(3 citation statements)

References 71 publications

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“…All VLP lattices with various sizes and shapes were captured even with irregular shapes (Figure 7e and Supplementary Movie 2), demonstrated TomoNet’s particle picking ability on flexible lattices. Lattice defects on each VLP were also identified consistent with previous studies 48 , enhancing the understanding of lattice assembly mechanisms 49 .…”

Section: Resultssupporting

confidence: 85%

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TomoNet: A streamlined cryoET software pipeline with automatic particle picking on flexible lattices

Wang,

Liao,

et al. 2024

Preprint

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Cryogenic electron tomography (cryoET) is capable of determining in situ biological structures of molecular complexes at near atomic resolution by averaging half a million subtomograms. While abundant complexes/particles are often clustered in arrays, precisely locating and seamlessly averaging such particles across many tomograms present major challenges. Here, we developed TomoNet, a software package with a modern graphical user interface to carry out the entire pipeline of cryoET and subtomogram averaging to achieve high resolution. TomoNet features built-in automatic particle picking and 3D classification functions and integrates commonly used packages to streamline high-resolution subtomogram averaging for structures in one-, two- or three-dimensional arrays. Automatic particle picking is accomplished in two complementary ways: one based on template matching and the other employing deep learning. TomoNet's hierarchical file organization and visual display facilitate efficient data management as required for large cryoET datasets. Applications of TomoNet to three types of datasets demonstrate its capability of efficient and accurate particle picking on flexible and imperfect lattices to obtain high-resolution 3D biological structures: virus-like particles, bacterial surface layers within cellular lamellae, and membranes decorated with nuclear egress protein complexes. These results demonstrate TomoNet's potential for broad applications to various cryoET projects targeting high-resolution in situ structures.

show abstract

Section: Resultssupporting

confidence: 85%

“…Lattice defects on each VLP were also identified consistent with previous studies 48 , enhancing the understanding of lattice assembly mechanisms 49 .…”

Section: Application To In Situ Viral Protein Arrays: the Matrix Prot...supporting

confidence: 85%

TomoNet: A streamlined cryoET software pipeline with automatic particle picking on flexible lattices

Wang,

Liao,

et al. 2024

Preprint

View full text Add to dashboard Cite

show abstract

“…Lattice defects on each VLP were also identified consistent with previous studies, 52 enhancing the understanding of lattice assembly mechanisms. 53…”

Section: Application To In Situ Viral Protein Arrays: the Matrix Prot...mentioning

confidence: 99%

TomoNet: A streamlined cryogenic electron tomography software pipeline with automatic particle picking on flexible lattices

Wang,

Liao,

et al. 2024

Biol. Imaging

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Cryogenic electron tomography (cryoET) is capable of determining in situ biological structures of molecular complexes at near-atomic resolution by averaging half a million subtomograms. While abundant complexes/particles are often clustered in arrays, precisely locating and seamlessly averaging such particles across many tomograms present major challenges. Here, we developed TomoNet, a software package with a modern graphical user interface to carry out the entire pipeline of cryoET and subtomogram averaging to achieve high resolution. TomoNet features built-in automatic particle picking and three-dimensional (3D) classification functions and integrates commonly used packages to streamline high-resolution subtomogram averaging for structures in 1D, 2D, or 3D arrays. Automatic particle picking is accomplished in two complementary ways: one based on template matching and the other using deep learning. TomoNet's hierarchical file organization and visual display facilitate efficient data management as required for large cryoET datasets. Applications of TomoNet to three types of datasets demonstrate its capability of efficient and accurate particle picking on flexible and imperfect lattices to obtain high-resolution 3D biological structures: virus-like particles, bacterial surface layers within cellular lamellae, and membranes decorated with nuclear egress protein complexes. These results demonstrate TomoNet's potential for broad applications to various cryoET projects targeting high-resolution in situ structures. Impact StatementCryogenic electron tomography (cryoET) has become a powerful approach to visualize the organization and high-resolution structures of biological complexes in their native environment. Subtomogram averaging (STA) of hundreds of thousands of particles (i.e., subtomograms) is necessary to obtain near-atomic resolution structures for each such complex. While abundant biological complexes often cluster in arrays that manifest as one to three-dimensional lattices, flexibility and imperfection of such lattices pose challenges for efficient and accurate particle picking. To overcome these challenges and to meet the growing demand for efficient data processing and management in the cryoET and STA workflow, we have developed TomoNet, a user-friendly software package with a modern graphical user interface that allows users to execute the entire data processing pipeline seamlessly with the integration of commonly used software packages. TomoNet addresses the particlepicking challenge with two solutions, one based on geometric template matching and the other using artificial intelligence. Applications of TomoNet to three representative datasets demonstrate its capability for highresolution structure determination of biological complexes on flexible and imperfect lattices.

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Structure of the HIV immature lattice allows for essential lattice remodeling within budded virions

Guo

Saha

Saffarian

et al. 2023

eLife

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For HIV virions to become infectious, the immature lattice of Gag polyproteins attached to the virion membrane must be cleaved. Cleavage cannot initiate without the protease formed by the homo-dimerization of domains linked to Gag. However, only 5% of the Gag polyproteins, termed Gag-Pol, carry this protease domain, and they are embedded within the structured lattice. The mechanism of Gag-Pol dimerization is unknown. Here, we use spatial stochastic computer simulations of the immature Gag lattice as derived from experimental structures, showing that dynamics of the lattice on the membrane is unavoidable due to the missing 1/3 of the spherical protein coat. These dynamics allow for Gag-Pol molecules carrying the protease domains to detach and reattach at new places within the lattice. Surprisingly, dimerization timescales of minutes or less are achievable for realistic binding energies and rates despite retaining most of the large-scale lattice structure. We derive a formula allowing extrapolation of timescales as a function of interaction free energy and binding rate, thus predicting how additional stabilization of the lattice would impact dimerization times. We further show that during assembly, dimerization of Gag-Pol is highly likely and therefore must be actively suppressed to prevent early activation. By direct comparison to recent biochemical measurements within budded virions, we find that only moderately stable hexamer contacts (-12kBT<∆G<-8kBT) retain both the dynamics and lattice structures that are consistent with experiment. These dynamics are likely essential for proper maturation, and our models quantify and predict lattice dynamics and protease dimerization timescales that define a key step in understanding formation of infectious viruses.

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HIV-2 Immature Particle Morphology Provides Insights into Gag Lattice Stability and Virus Maturation

Cited by 3 publications

References 71 publications

TomoNet: A streamlined cryoET software pipeline with automatic particle picking on flexible lattices

TomoNet: A streamlined cryoET software pipeline with automatic particle picking on flexible lattices

TomoNet: A streamlined cryogenic electron tomography software pipeline with automatic particle picking on flexible lattices

Structure of the HIV immature lattice allows for essential lattice remodeling within budded virions

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