ArticleStructure (London, England : 1993)2015
Atomic Modeling of an Immature Retroviral Lattice Using Molecular Dynamics and Mutagenesis.
Article in Structure (London, England : 1993), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Mechanistic insights into CAM-induced disruption of HBV capsids revealed by all-atom MD simulations.PLoS pathogens · 2026Article
- Transient Occupancy and Pore Dynamics: IP6 Behavior in HIV-1The journal of physical chemistry. B · 2026Article
- Mechanistic insights into CAM-induced disruption of HBV capsids revealed by all-atom MD simulations.bioRxiv : the preprint server for biology · 2025Article
- Review
- Article
- The impact of Gag non-cleavage site mutations on HIV-1 viral fitness from integrative modelling and simulations.Computational and structural biotechnology journal · 2021Article
- Scalable molecular dynamics on CPU and GPU architectures with NAMD.The Journal of chemical physics · 2020Article
- Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly.PLoS pathogens · 2020Article
- All-atom virus simulations.Current opinion in virology · 2018Review
- Article
- Article
- Quenching protein dynamics interferes with HIV capsid maturation.Nature communications · 2017Article
- A Large Size Chimeric Highly Immunogenic Peptide Presents Multistage Plasmodium Antigens as a Vaccine Candidate System against Malaria.Molecules (Basel, Switzerland) · 2017Article
- All-Atom Molecular Dynamics Simulations of Entire Virus Capsid Reveal the Role of Ion Distribution in Capsid's Stability.The journal of physical chemistry letters · 2017Article
- A chimeric protein-based malaria vaccine candidate induces robust T cell responses against Plasmodium vivax MSP1Scientific reports · 2016Article
- Functional Equivalence of Retroviral MA Domains in Facilitating Psi RNA Binding Specificity by Gag.Viruses · 2016Article
- Molecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy maps.eLife · 2016Article
- Computational Methodologies for Real-Space Structural Refinement of Large Macromolecular Complexes.Annual review of biophysics · 2016Review
- Computational virology: From the inside out.Biochimica et biophysica acta · 2016Review
- Contributions of Charged Residues in Structurally Dynamic Capsid Surface Loops to Rous Sarcoma Virus Assembly.Journal of virology · 2016Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Defining the molecular interaction between Gag proteins in an assembled hexagonal lattice of immature retrovirus particles is crucial for elucidating the mechanisms of virus assembly and maturation. Recent advances in cryo-electron microscopy have yielded subnanometer structural information on the morphology of immature Gag lattices, making computational modeling and simulations feasible for investigating the Gag-Gag interactions at the atomic level. We have examined the structure of Rous sarcoma virus (RSV) using all-atom molecular dynamics simulations and in vitro assembly, to create the first all-atom model of an immature retroviral lattice. Microseconds-long replica exchange molecular dynamics simulation of the spacer peptide (SP)-nucleocapsid (NC) subdomains results in a six-helix bundle with amphipathic properties. The resulting model of the RSV Gag lattice shows features and dynamics of the capsid protein with implications for the maturation process, and confirms the stabilizing role of the upstream and downstream regions of Gag, namely p10 and SP-NC.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.