Atomic Modeling of an Immature Retroviral Lattice Using Molecular Dynamics and Mutagenesis

Boon Chong Goh, Juan R. Perilla, Matthew R. England, Katrina J. Heyrana, Rebecca C. Craven, Klaus Schulten

Research output: Contribution to journalArticlepeer-review

27 Scopus citations

Abstract

Summary 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.

Original languageEnglish (US)
Article number3201
Pages (from-to)1414-1425
Number of pages12
JournalStructure
Volume23
Issue number8
DOIs
StatePublished - Aug 7 2015

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Molecular Biology

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