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.