1. Building: An initial integrative model of the NPC was enriched by incorporating an explicit membrane environment and filling it with intrinsically disordered protein (IDP) components, specifically FG-Nups, which form the hydrophobic diffusion barrier of the pore. Simultaneously, the positions of the individual subunits of the HIV capsid were identified using template matching into cryo-electron tomograms. These subunits were then fitted into their respective positions to create a detailed atomic model of the HIV capsid.

2. Simulation: The enriched model was allowed to evolve over time using molecular dynamics (MD) simulations, with parameters tuned to match experimental data, particularly the interaction strength of the IDP domains, which was calibrated to Förster resonance energy transfer (FRET) measurements of their conformation. The capsid structure was similarly refined, allowing side chains to relax in a full-atom MD simulation. The two models were then merged based on snapshots of HIV capsid positions relative to the nuclear pore, as observed in cryo-electron tomography (cryo-ET) images of infected cells. The combined models, incorporating both the capsid and the nuclear pore in varying diameters, were further evolved over time using coarse-grained MD simulations.

3. Evaluation: These simulations yielded several key predictions. They identified the specific positions where the HIV capsid advances within the nuclear pore until it reaches an energy minimum, the extent to which FG-Nups can be deformed in various dilation states before clashing with the capsid, and, crucially, that dilation of the NPC to a physiological diameter alone is insufficient to allow the intact HIV capsid to pass through. Experimental observations using cryo-ET of infected cells confirmed that the nuclear pore must crack during capsid passage. Further simulations with cracked nuclear pores supported the idea that this structural change is necessary for the capsid’s successful translocation. These findings encourage further research to identify factors in the nucleoplasm that might facilitate the capsid’s opening and its deeper entry into the chromatin.