Nuclear Entry of HIV Conceptualized Through
a Digital Twin
To initiate infection, the human immunodeficiency virus (HIV) must deliver its genetic material into the nucleus of a human host cell. However, the HIV capsid is approximately 20 nm larger in diameter than the nuclear pore complex (NPC). Earlier models hypothesized that the capsid disintegrates on the cytoplasmic side, releasing viral RNA through the NPC into the nucleus.
Using iterative digital twin cycles, we aim to address the question: How does HIV transport its genetic information through the nuclear pore complex?
Step 1: Building (Cycle 1)
Based on a previous structural model and in vivo single molecule fluorescence resonance energy transfer (FRET) data, an advanced model of the NPC was generated, detailing its structure and the obstructive role of FG-Nups (FG-nucleoporins) that line the pore (Bui, … Beck, Cell 2013; Kosinski, … Beck, Science 2016; Mosalaganti, … Hummer, Kosinski, Beck; Yu, … Beck, Hummer, Lemke, Nature 2023). Cryo-electron tomography (cryo-ET) imaging of HIV-infected cells was conducted to observe capsid disintegration events near the NPC, as predicted by prior hypotheses. Subtomogram averaging confirmed that due to the NPC's size constraints and FG-Nup obstruction, an intact HIV capsid could not pass through NPC. Furthermore, no instances of capsid disintegration were observed, challenging earlier models and suggesting that prior assumptions regarding HIV nuclear entry were incorrect.
Step 2: Simulating (Cycle 1)
A refined model incorporating the HIV capsid with the NPC was generated to explore the possibility of intact capsid passage. Molecular dynamics (MD) simulations indicated that, under these conditions, intact capsid passage through the NPC was unfeasible. This raised a critical question: How does the intact HIV capsid cross the NPC?
Step 3: Evaluating (Cycle 1)
Super-resolution imaging of HIV-infected cells revealed the presence of HIV capsids on both the cytoplasmic and nuclear sides of the NPC, with some capsids found within the NPC. Correlative light and electron microscopy (CLEM) data further confirmed that intact capsids could indeed enter the nucleus. This led to a revised hypothesis: If structural changes occur within the NPC, intact HIV capsids may be able to traverse it. Template matching was adjusted, focusing on NPC subunits with non-symmetrical architectures (Cruz-León, … Beck, Turoňová, Hummer, Nature Communications 2024). Subtomogram averaging revealed NPCs exhibiting structural irregularities, or “cracks,” with some capsids located deep within these damaged NPCs, suggesting that structural disruptions might permit intact capsid passage.
Step 1: Building (Cycle 2)
With this new data, enriched HIV-NPC interaction models were refined, taking in account parameters such as capsid movement within the NPC and the extent to which FG-Nups could deform before interacting with the capsid were fine-tuned. Various models were developed to simulate different sizes of cracks in the NPC that could allow HIV capsid passage.
Step 2: Simulating (Cycle 2)
The updated MD simulations indicated that NPC dilation alone is insufficient to permit intact HIV capsid passage (Kreysing, … Turoňová, Hummer, Kräusslich, Beck, Cell 2025). However, if the NPC develops substantial structural cracks, the capsid may traverse the pore, as the cracks alleviate the NPC’s size constraints and FG-Nup interference.
Step 3: Evaluating (Cycle 2)
These findings prompt further questions: What occurs with the HIV capsid once it is within the nucleus? Related inquiries within the SCALE cluster include: How are large cargos, such as mRNA, exported from the nucleus? What conformational changes are essential for NPCs to transport cargos of varying sizes? Using iterative, self-refining digital twin cycles, we aim to address these challenging questions.
