ArticleBiophysical journal2010
Multiscale computer simulation of the immature HIV-1 virion.
Article in Biophysical journal, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- Exploring putative drug properties associated with TNF-alpha inhibition and identification of potential targets in cardiovascular disease using machine learning-assisted QSAR modeling and virtual reverse pharmacology approach.Molecular diversity · 2024Article
- Temporal control by cofactors prevents kinetic trapping in retroviral Gag lattice assembly.Biophysical journal · 2023Article
- Structure of the HIV immature lattice allows for essential lattice remodeling within budded virions.eLife · 2023Article
- Understanding Virus Structure and Dynamics through Molecular Simulations.Journal of chemical theory and computation · 2023Review
- Tripartite efflux pumps of the RND superfamily: what did we learn from computational studies?Microbiology (Reading, England) · 2023Review
- Molecular dynamics of the viral life cycle: progress and prospects.Current opinion in virology · 2021Review
- Identifying crucial E-protein residues responsible for unusual stability of Zika virus envelope.Biophysical journal · 2021Article
- Integrative structural biology of HIV-1 capsid protein assemblies: combining experiment and computation.Current opinion in virology · 2021Review
- The impact of Gag non-cleavage site mutations on HIV-1 viral fitness from integrative modelling and simulations.Computational and structural biotechnology journal · 2021Article
- NERDSS: A Nonequilibrium Simulator for Multibody Self-Assembly at the Cellular Scale.Biophysical journal · 2020Article
- Mesoscale All-Atom Influenza Virus Simulations Suggest New Substrate Binding Mechanism.ACS central science · 2020Article
- Integrative modeling of the HIV-1 ribonucleoprotein complex.PLoS computational biology · 2019Article
- Emerging Diversity in Lipid-Protein Interactions.Chemical reviews · 2019Review
- Computational Modeling of Realistic Cell Membranes.Chemical reviews · 2019Review
- All-atom virus simulations.Current opinion in virology · 2018Review
- Communication: Adaptive boundaries in multiscale simulations.The Journal of chemical physics · 2018Article
- Article
- Immature HIV-1 lattice assembly dynamics are regulated by scaffolding from nucleic acid and the plasma membrane.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Multiscale simulations of protein-facilitated membrane remodeling.Journal of structural biology · 2016Review
- Computational virology: From the inside out.Biochimica et biophysica acta · 2016Review
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Multiscale computer simulations, employing a combination of experimental data and coarse-graining methods, are used to explore the structure of the immature HIV-1 virion. A coarse-grained (CG) representation is developed for the virion membrane shell and Gag polypeptides using molecular level information. Building on the results from electron cryotomography experiments, the simulations under certain conditions reveal the existence of an incomplete p6 hexameric lattice formed from hexameric bundles of the Gag CA domains. In particular, the formation and stability of the immature Gag lattice at the CG level requires enhanced interfacial interactions of the CA protein C-terminal domains (CTDs). An exact mapping of the CG representation back to the molecular level then allows for detailed atomistic molecular dynamics studies to confirm the existence of these enhanced CA(CTD) interactions and to probe their possible origin. The multiscale simulations further provide insight into potential CA(CTD) mutations that may disrupt or modify the Gag immature lattice assembly process in the immature HIV-1 virion.
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