Understanding the host cell surface receptor recognition by adeno associated virus 2 capsid protein and its modulation through allostery-driven mutations: An integrative modelling and simulation approach

AAV (Adeno Associated Virus) vectors have emerged as a promising approach for efficient gene delivery in vivo, and AAV capsid engineering is required to achieve transduction efficiency and bypass pre-existing immunity. However, a lack of knowledge of the host receptor recognition mechanism of AAVs seriously impedes structure-guided rational engineering. Here, we explored the mechanism of a well-known host receptor, AAVR, with two Immunoglobulin (Ig)-like PKD domains (PKD1 and 2) recognition by AAV2 capsid protein using a combination of coarse-grained multi-state elastic network dynamics, all-atom molecular dynamics simulation, and binding free energy calculations. Our data suggest that the PKD2 domain interacts robustly with AAV2, while PKD1 is a low-affinity capsid binder. The orientation of PKDs on the capsid surface is complex and involves two adjacent 3-fold axes. PKD domain docking sites and the critical hotspot residues involved have been identified using all-atom and coarse-grained MD simulations. We observed that AAVR binding induces long-range allostery-mediated structural dynamics in the AAV2 capsid protein. We have decoded the communication network between the receptor binding sites and allosteric sites. Harnessing the residue interaction network, we generated capsid protein mutants with predicted improved host receptor binding abilities, demonstrated by equilibrium simulation and steered molecular dynamics.