The full activation mechanism of the adenosine A(1) receptor revealed by GaMD and Su-GaMD simulations

The full activation process of G protein–coupled receptor (GPCR) plays an important role in cellular signal transduction. However, it remains challenging to simulate the whole process in which the GPCR is recognized and activated by a ligand and then couples to the G protein on a reasonable simulation timescale. Here, we developed a molecular dynamics (MD) approach named supervised (Su) Gaussian accelerated MD (GaMD) by incorporating a tabu-like supervision algorithm into a standard GaMD simulation. By using this Su-GaMD method, from the active and inactive structure of adenosine A(1) receptor (A(1)R), we successfully revealed the full activation mechanism of A(1)R, including adenosine (Ado)–A(1)R recognition, preactivation of A(1)R, and A(1)R–G protein recognition, in hundreds of nanoseconds of simulations. The binding of Ado to the extracellular side of A(1)R initiates conformational changes and the preactivation of A(1)R. In turn, the binding of G(i2) to the intracellular side of A(1)R causes a decrease in the volume of the extracellular orthosteric site and stabilizes the binding of Ado to A(1)R. Su-GaMD could be a useful tool to reconstruct or even predict ligand–protein and protein–protein recognition pathways on a short timescale. The intermediate states revealed in this study could provide more detailed complementary structural characterizations to facilitate the drug design of A(1)R in the future.