Competitive binding and geometric changes allow fast, complete translocation of intact HIV-1 capsids through the nuclear pore complex

Abstract

Recent experiments on HIV-1 capsid translocation through the nuclear pore complex (NPC) have demonstrated the docking of intact or nearly intact capsids at the pore, followed by translocation, with capsid disassembly occurring only within the nucleus near the site of integration. Given that the size of the capsid is comparable to the pore dimensions, these new findings raise questions regarding the energetics and dynamics of capsid passage across the significant entropic barrier created by the disordered FG nucleoporins (FG nups) in the NPC central channel. Here, we develop an analytical model for the transport of the HIV-1 capsid that considers the geometry of the capsid and pore, the free energy barrier due to the FG nups, and capsid-nup interactions. Our results show that capsid entry into the pore is favorable if the narrow end enters first, consistent with experimental observations, and that increasing the capsid-nup interaction strength enhances inward capsid flux. However, capsid-nup interaction alone is insufficient for complete capsid nuclear import and competitive binding by the nuclear factor CPSF6 to FG-binding sites on the capsid can serve as a ratcheting mechanism for full nuclear import. We show that nuclear import is arrested below a minimum CPSF6 concentration, consistent with experimental observations, and that pore dilation or capsid deformation can accelerate the translocation process. Our work explores the physics underlying a new perspective on HIV-1 viral genome nuclear import and provides quantitative explanations for experimentally observed phenomena while making testable predictions. Significance statementHIV-1 remains a devastating global health threat, with millions of new infections each year. However, the mechanism by which the viral genome enters the host nucleus is still not fully understood. Recent experiments show that the HIV-1 capsid can remain intact - or nearly so - during nuclear import, challenging long-held assumptions about the limits on size for transport through the nuclear pore. Here, we present a biophysical model that explains the directional transport of the capsid, the role of capsid and pore geometry and host factors such as CPSF6, and elucidates a ratcheting mechanism that allows entry of intact capsids within physiological timescales. This work provides a mechanistic framework for a critical step in the early stages of HIV-1 infection.