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Abstract
During HIV-1 maturation, CA can self-assemble into a wide range of capsid morphologies made of ~175-250 hexamers and 12 pentamers. Most recently, the cellular polyanion inositol hexakisphosphate (IP6) has been demonstrated to facilitate conical capsid formation by coordinating a ring of arginine residues within the central cavity of capsid hexamers and pentamers. However, the precise kinetic interplay of events during IP6 and CA co-assembly is unclear. In the first project, we use Coarse-grained Molecular Dynamics (CGMD) simulations to elucidate the underlying molecular mechanism of capsid formation, including the crucial role played by IP6. We show that IP6, in relatively small quantities at first, promotes curvature generation by trapping pentameric defects in the growing lattice and shifts assembly behavior towards kinetically favored outcomes. Our analysis also suggests that IP6 can stabilize metastable capsid intermediates and can induce structural pleomorphism in mature capsids. Relatedly, A structural switch comprising the Thr-Val-Gly-Gly (TVGG) motif either assumes a disordered coil or a helix conformation to regulate hexamer or pentamer assembly, respectively. Both IP6 binding and TVGG coil-to-helix transition are essential for pentamer formation. However, the correlation between IP6 binding at the pore and mechanistic details of coil-to-helix transition in pentamer have not been elucidated. Using extensive all-atom molecular dynamics simulations and structural analysis, we demonstrate that IP6 binding at the pore triggers a network of interactions downstream. IP6 imparts structural order at the central ring, which results in multiple kinetically controlled events leading to the coil-to-helix conformational change of the TVGG motif. IP6 facilitates the helix-to-coil transition by allowing the formation of intermediate conformations. Our results identify the key kinetic role of IP6 in pentamer formation, which facilitates the capsid assembly. These results also may point to new druggable targets to prevent intact HIV-1 core formation. For example, small molecule Lenacapavir (LEN) has been proposed to disrupt capsid morphogenesis by occupying the FG-binding pocket located between neighboring CA subunits. As LEN and IP6 interact with overlapping structural elements, they can compete to influence the assembly pathway and outcomes. Using coarse-grained molecular simulations, we examined capsid assembly across varying IP6 and LEN conditions. Our results reveal a concentration-dependent shift in assembly outcomes: LEN accelerates hexamer assembly and reduces pentamer incorporation, leading to malformed, multilayered, or incomplete capsids. Simulations including the viral RNP further show that LEN-treated capsids frequently fail to encapsidate the RNA genome, indicating impaired maturation. Our calculations confirm that LEN impairs the formation of high-curvature regions necessary for closure, supporting a model of off-pathway assembly as a mechanism of viral inhibition. Building on these findings, we developed a bottom-up coarse-grained modeling framework to investigate the interaction of the HIV-1 capsid with host factors during nuclear entry. We constructed and simulated CG models of the capsid in complex with cyclophilin A, Nup358, and Nup153. Our results reveal that while moderate levels of CypA binding stabilize the capsid, excessive CypA coating induces asymmetric strain and structural collapse, particularly at the narrow tip. Simulations of Nup358 domains captured known structural features such as the S-shaped N-terminal solenoid and the oligomerization-driven filament formation via the OE domain. We further modeled Nup153-mediated interactions at the nuclear basket and observed multivalent FG-pocket binding and weak Nup153 self-association, suggesting a possible role in directional capsid translocation and mesh formation. These findings provide a unified view of HIV-1 capsid behavior across multiple stages of viral replication, from self-assembly to nuclear import. The integrative modeling approach presented here lays a foundation for future investigations into viral uncoating, host restriction and antiviral design targeting capsid-host interactions.