Mechanism of the G-protein mimetic nanobody binding to a muscarinic G-protein-coupled receptor

Significance Protein–protein interactions are important in cellular signaling. However, they have presented a challenge for molecular dynamics (MD) simulations, due to increased system complexity and slowly evolving dynamics. In particular, binding of the medically important G-protein-coupled receptors (GPCRs) with intracellular signaling proteins has not been simulated with MD to date. In this study, we performed long-timescale enhanced MD simulations using the Gaussian accelerated MD (GaMD) method on the M 2 muscarinic GPCR. The simulations revealed pathways and important low-energy intermediate states of the G-protein mimetic nanobody binding to the M 2 receptor. Our simulation results are consistent with experimental data and provide important insights into the GPCR–nanobody binding mechanism. GaMD is thus applicable to enhanced simulations of protein–protein interactions.