Theoretical Design and Structural Characterization of Cross-Genera AAVGo.1-HBoV3 Chimeric Capsids

Parvoviruses are small, non-enveloped DNA viruses, several of which have been adapted as vectors for gene therapy. Adeno-associated virus (AAV) is clinically established but constrained by limited genome capacity and pre-existing immunity. Human bocaviruses (HBoVs) possess larger packaging potential and airway tropism, motivating exploration of AAV-HBoV hybrid architectures. We modeled a chimeric construct (AAV-HB3) in which the α-helix and βI strand of AAVGo.1 were replaced with the corresponding regions from HBoV3. AlphaFold2 predictions (pLDDT > 80, pTM > 0.75) confirmed retention of the β-barrel scaffold, and RoseTTAFold2 refinement produced energetically stable conformations. 100 ns molecular-dynamics simulations showed distinct dynamic profiles: the AAVGo.1 VP1 control remained conformationally rigid (RMSD ≈ 0.03 nm), whereas AAV-HB3 exhibited increased flexibility at VR-VIII, VR-IV, and the HI loop, with loop displacements of ~43–54 Å localized near the three-fold and five-fold symmetry axes. These structure-based analyses define how cross-genera substitutions redistribute local flexibility within the parvoviral capsid, providing a predictive framework for engineering next-generation vectors with assessing structural tolerance relevant to capsid.