Role of viral protein ratio in the structure and separation of empty and full adeno-associated virus capsids: A molecular dynamics study

The effects of viral capsid protein (VP) composition on adeno-associated virus (AAV) structure are investigated by molecular simulations, with a specific focus on the separation mechanism of empty and full AAV capsids in anion-exchange chromatography. We used AlphaFold predictions and all-atom molecular dynamics simulations to study AAV-LK03 capsids for different capsid configurations. AlphaFold predicts a structured and an unstructured unique region for the VP1 (VP1u) and the VP2 (VP2u) proteins, respectively. Simulations of entire capsids show that increasing the VP1 content would likely impair transgene loading, consistent with the measured higher VP1 content of empty than full capsids. Our experimental characterization also shows that increased VP1/VP2 content correlates with reduced transgene loading. Simulations also reveal that, because the VP1u/VP2u regions are internalized, the effects of VP1/VP2 ratios on the external surface potential of capsids and hence the capsid separation in ion-exchange chromatography should be minimal. However, transgene loading would be expected to push the VP1u/VP2u domains toward the inner surface of the 5-fold axis, which simulations show would change the surface topography to expose more negative charge on the surface for full capsids with greater VP1/VP2 content. These molecular insights can inform future strategies for AAV vector development and purification. Molecular simulations are used to reveal the impact of viral protein composition on AAV retention in ion-exchange chromatography. Higher ratios of VP1/VP2 can impair transgene loading. While VP ratio has a minimal effect on retention of empty capsids, it can affect the surface characteristics for full capsids due to the presence of the transgene.