Figure 3.

CG simulation snapshots of planar self-assembly for the model HIV-1 CA dimer lattice. NTDs are colored by association with hexamers (light gray, green online), pentamers (medium gray, red online), and trimer-of-dimers (dark gray, blue online); when the NTDs are part of both a trimer-of-dimers and a pentamer or hexamer, the color is that of a pentamer or hexamer. Monomers that are not associated with the three structure types are omitted for clarity. (A) Early stage of a flexible dimer simulation with the three major structural motifs present (left) and later stage of same simulation, with the onset of mature p6 lattice formation visible (right). (B) Rigid dimer interface simulations showing enhanced trimer-of-dimers presence and the manner in which such structures may combine via native NTD-NTD and NTD-CTD contacts to form mature lattice precursors. (C) All-atom representation of the trimer-of-dimers structure, with CTD dimer interfaces indicated with lines and the location of NTD hexamer rings indicated with hexagons. Also shown is the CG representation of the trimer-of-dimers structure, with the location in a region of mature-style p6 lattice indicated by the triangle (same color scheme as in A and B). All simulations at ρ = 0.5, with A and B showing two periodic images.