Unveiling the structural properties of HIV-1 vesicle from atomistic molecular dynamics simulations

The HIV-1 viral particle contains all the macromolecular components to infect host cells,
typically CD4 + T human cells, by fusion of the viral envelope with the cell plasma membrane.
Such macromolecular components correspond to phospholipids, membrane glycoproteins,
genomic RNA, and gag polyproteins; which are assembled during infection to furthermore
undergo maturation and structural re-arrangements to form the virion. Here, exploiting the
advances of molecular modeling, we present the first insights towards the construction of an
all-atomistic model of the HIV-1 mature and immature virion. The model includes a twenty-
four lipids bilayer with membrane glycoproteins, and the capsid protein. We review over the
techniques proposed to build and prepare the system, as well as the steps required to
simulate, analyze and characterize the HIV-1 virion model, which contains over 800 million
atoms.